diff --git a/.gitea/workflows/build.yaml b/.gitea/workflows/build.yaml
index 732fb75..45aa628 100644
--- a/.gitea/workflows/build.yaml
+++ b/.gitea/workflows/build.yaml
@@ -13,7 +13,7 @@ jobs:
uses: actions/checkout@v3
- run: echo "The ${{ github.repository }} repository has been cloned to the runner."
- run: echo "The workflow is now ready to test your code on the runner."
- - name: List files in the repository
+ - name: List files in the repository:
run: |
ls ${{ github.workspace }}
- run: echo "This job's status is ${{ job.status }}."
diff --git a/Dockerfile b/Dockerfile
index 9f88544..a5d1263 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,63 +1,57 @@
################## First Stage - Creating base #########################
# Created a variable to hold our node base image
-ARG NODE_IMAGE=node:22-trixie-slim
+ARG NODE_IMAGE=node:22-bookworm-slim
FROM $NODE_IMAGE AS base
-
# Install dumb-init and ClamAV, and perform ClamAV database update
-RUN apt-get update \
- && apt-get install -y --no-install-recommends \
- dumb-init \
- clamav \
- clamav-daemon \
- clamdscan \
- ca-certificates \
+RUN apt update \
+ && apt-get install -y dumb-init clamav clamav-daemon nano \
&& rm -rf /var/lib/apt/lists/* \
# Creating folders and changing ownerships
- && mkdir -p /home/node/app \
- && mkdir -p /var/lib/clamav \
+ && mkdir -p /home/node/app && chown node:node /home/node/app \
+ && mkdir -p /var/lib/clamav \
&& mkdir /usr/local/share/clamav \
+ && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav \
+ # permissions
&& mkdir /var/run/clamav \
- && mkdir -p /var/log/clamav \
- && mkdir -p /tmp/clamav-logs \
-
- # Set ownership and permissions
- && chown node:node /home/node/app \
- # && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav \
- && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \
- && chown -R node:clamav /etc/clamav \
- && chmod 755 /tmp/clamav-logs \
- && chmod 750 /var/run/clamav \
- && chmod 755 /var/lib/clamav \
- && chmod 755 /var/log/clamav \
- # Add node user to clamav group and allow sudo for clamav commands
- && usermod -a -G clamav node
- # && chmod 666 /var/run/clamav/clamd.socket
- # Make directories group-writable so node (as member of clamav group) can access them
- # && chmod 750 /var/run/clamav /var/lib/clamav /var/log/clamav /tmp/clamav-logs
+ && chown node:clamav /var/run/clamav \
+ && chmod 750 /var/run/clamav
+# -----------------------------------------------
+# --- ClamAV & FeshClam -------------------------
+# -----------------------------------------------
+# RUN \
+# chmod 644 /etc/clamav/freshclam.conf && \
+# freshclam && \
+# mkdir /var/run/clamav && \
+ # chown -R clamav:root /var/run/clamav
+# # initial update of av databases
+# RUN freshclam
-# Configure ClamAV - copy config files before switching user
-# COPY --chown=node:clamav ./*.conf /etc/clamav/
+# Configure Clam AV...
COPY --chown=node:clamav ./*.conf /etc/clamav/
-
-
+# # permissions
+# RUN mkdir /var/run/clamav && \
+# chown node:clamav /var/run/clamav && \
+# chmod 750 /var/run/clamav
# Setting the working directory
WORKDIR /home/node/app
# Changing the current active user to "node"
-
-# Download initial ClamAV database as root before switching users
USER node
-RUN freshclam --quiet || echo "Initial database download failed - will retry at runtime"
-# Copy entrypoint script
+# initial update of av databases
+RUN freshclam
+
+# VOLUME /var/lib/clamav
COPY --chown=node:clamav docker-entrypoint.sh /home/node/app/docker-entrypoint.sh
RUN chmod +x /home/node/app/docker-entrypoint.sh
ENV TZ="Europe/Vienna"
+
+
################## Second Stage - Installing dependencies ##########
# In this stage, we will start installing dependencies
FROM base AS dependencies
@@ -76,6 +70,7 @@ ENV NODE_ENV=production
# We run "node ace build" to build the app (dist folder) for production
RUN node ace build --ignore-ts-errors
# RUN node ace build --production
+# RUN node ace build --ignore-ts-errors
################## Final Stage - Production #########################
@@ -93,7 +88,6 @@ RUN npm ci --omit=dev
# Copy files to the working directory from the build folder the user
COPY --chown=node:node --from=build /home/node/app/build .
# Expose port
-# EXPOSE 3310
EXPOSE 3333
ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
# Run the command to start the server using "dumb-init"
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index 23bb390..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,22 +0,0 @@
-
-MIT License
-
-Copyright (c) 2025 Tethys Research Repository
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE
\ No newline at end of file
diff --git a/adonisrc.ts b/adonisrc.ts
index 824d4c8..19e946c 100644
--- a/adonisrc.ts
+++ b/adonisrc.ts
@@ -11,10 +11,9 @@ export default defineConfig({
*/
commands: [
- () => import('@adonisjs/core/commands'),
- () => import('@adonisjs/lucid/commands'),
- () => import('@adonisjs/mail/commands')
- ],
+ () => import('@adonisjs/core/commands'),
+ () => import('@adonisjs/lucid/commands'),
+ () => import('@adonisjs/mail/commands')],
/*
|--------------------------------------------------------------------------
| Preloads
@@ -27,17 +26,16 @@ export default defineConfig({
() => import('./start/routes.js'),
() => import('./start/kernel.js'),
() => import('#start/validator'),
- // () => import('#start/rules/unique'),
- // () => import('#start/rules/translated_language'),
- // () => import('#start/rules/unique_person'),
- // // () => import('#start/rules/file_length'),
- // // () => import('#start/rules/file_scan'),
- // // () => import('#start/rules/allowed_extensions_mimetypes'),
- // () => import('#start/rules/dependent_array_min_length'),
- // () => import('#start/rules/referenceValidation'),
- // () => import('#start/rules/valid_mimetype'),
- // () => import('#start/rules/array_contains_types'),
- // () => import('#start/rules/orcid'),
+ () => import('#start/rules/unique'),
+ () => import('#start/rules/translated_language'),
+ () => import('#start/rules/unique_person'),
+ () => import('#start/rules/file_length'),
+ () => import('#start/rules/file_scan'),
+ () => import('#start/rules/allowed_extensions_mimetypes'),
+ () => import('#start/rules/dependent_array_min_length'),
+ () => import('#start/rules/referenceValidation'),
+ () => import('#start/rules/valid_mimetype'),
+ () => import('#start/rules/array_contains_types'),
],
/*
|--------------------------------------------------------------------------
@@ -72,7 +70,7 @@ export default defineConfig({
() => import('#providers/stardust_provider'),
() => import('#providers/query_builder_provider'),
() => import('#providers/token_worker_provider'),
- () => import('#providers/rule_provider'),
+ // () => import('#providers/validator_provider'),
// () => import('#providers/drive/provider/drive_provider'),
() => import('@adonisjs/drive/drive_provider'),
// () => import('@adonisjs/core/providers/vinejs_provider'),
diff --git a/app/Controllers/Http/Admin/mailsettings_controller.ts b/app/Controllers/Http/Admin/mailsettings_controller.ts
index 628a9fc..43e9dc7 100644
--- a/app/Controllers/Http/Admin/mailsettings_controller.ts
+++ b/app/Controllers/Http/Admin/mailsettings_controller.ts
@@ -76,24 +76,23 @@ export default class MailSettingsController {
public async sendTestMail({ response, auth }: HttpContext) {
const user = auth.user!;
const userEmail = user.email;
-
+
// let mailManager = await app.container.make('mail.manager');
- // let iwas = mailManager.use();
+ // let iwas = mailManager.use();
// let test = mail.config.mailers.smtp();
if (!userEmail) {
return response.badRequest({ message: 'User email is not set. Please update your profile.' });
}
try {
- await mail.send(
- (message) => {
- message
- // .from(Config.get('mail.from.address'))
- .from('tethys@geosphere.at')
- .to(userEmail)
- .subject('Test Email')
- .html('
If you received this email, the email configuration seems to be correct.
');
- });
+ await mail.send((message) => {
+ message
+ // .from(Config.get('mail.from.address'))
+ .from('tethys@geosphere.at')
+ .to(userEmail)
+ .subject('Test Email')
+ .html('If you received this email, the email configuration seems to be correct.
');
+ });
return response.json({ success: true, message: 'Test email sent successfully' });
// return response.flash('Test email sent successfully!', 'message').redirect().back();
diff --git a/app/Controllers/Http/Api/AuthorsController.ts b/app/Controllers/Http/Api/AuthorsController.ts
index 2b0bae1..7209699 100644
--- a/app/Controllers/Http/Api/AuthorsController.ts
+++ b/app/Controllers/Http/Api/AuthorsController.ts
@@ -4,29 +4,20 @@ import Person from '#models/person';
// node ace make:controller Author
export default class AuthorsController {
- public async index({}: HttpContext) {
-
+ public async index({}: HttpContext) {
+ // select * from gba.persons
+ // where exists (select * from gba.documents inner join gba.link_documents_persons on "documents"."id" = "link_documents_persons"."document_id"
+ // where ("link_documents_persons"."role" = 'author') and ("persons"."id" = "link_documents_persons"."person_id"));
const authors = await Person.query()
- .select([
- 'id',
- 'academic_title',
- 'first_name',
- 'last_name',
- 'identifier_orcid',
- 'status',
- 'name_type',
- 'created_at'
- // Note: 'email' is omitted
- ])
- .preload('datasets')
- .where('name_type', 'Personal')
- .whereHas('datasets', (dQuery) => {
- dQuery.wherePivot('role', 'author');
- })
- .withCount('datasets', (query) => {
- query.as('datasets_count');
- })
- .orderBy('datasets_count', 'desc');
+ .preload('datasets')
+ .where('name_type', 'Personal')
+ .whereHas('datasets', (dQuery) => {
+ dQuery.wherePivot('role', 'author');
+ })
+ .withCount('datasets', (query) => {
+ query.as('datasets_count');
+ })
+ .orderBy('datasets_count', 'desc');
return authors;
}
diff --git a/app/Controllers/Http/Api/AvatarController.ts b/app/Controllers/Http/Api/AvatarController.ts
index d7c532f..74fe135 100644
--- a/app/Controllers/Http/Api/AvatarController.ts
+++ b/app/Controllers/Http/Api/AvatarController.ts
@@ -2,46 +2,26 @@ import type { HttpContext } from '@adonisjs/core/http';
import { StatusCodes } from 'http-status-codes';
import redis from '@adonisjs/redis/services/main';
-const PREFIXES = ['von', 'van', 'de', 'del', 'della', 'di', 'da', 'dos', 'du', 'le', 'la'];
+const PREFIXES = ['von', 'van'];
const DEFAULT_SIZE = 50;
-const MIN_SIZE = 16;
-const MAX_SIZE = 512;
const FONT_SIZE_RATIO = 0.4;
const COLOR_LIGHTENING_PERCENT = 60;
const COLOR_DARKENING_FACTOR = 0.6;
-const CACHE_TTL = 24 * 60 * 60; // 24 hours instead of 1 hour
export default class AvatarController {
public async generateAvatar({ request, response }: HttpContext) {
try {
const { name, size = DEFAULT_SIZE } = request.only(['name', 'size']);
-
- // Enhanced validation
- if (!name || typeof name !== 'string' || name.trim().length === 0) {
- return response.status(StatusCodes.BAD_REQUEST).json({
- error: 'Name is required and must be a non-empty string',
- });
- }
-
- const parsedSize = this.validateSize(size);
- if (!parsedSize.isValid) {
- return response.status(StatusCodes.BAD_REQUEST).json({
- error: parsedSize.error,
- });
+ if (!name) {
+ return response.status(StatusCodes.BAD_REQUEST).json({ error: 'Name is required' });
}
// Build a unique cache key for the given name and size
- const cacheKey = `avatar:${this.sanitizeName(name)}-${parsedSize.value}`;
- // const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`;
- try {
- const cachedSvg = await redis.get(cacheKey);
- if (cachedSvg) {
- this.setResponseHeaders(response);
- return response.send(cachedSvg);
- }
- } catch (redisError) {
- // Log redis error but continue without cache
- console.warn('Redis cache read failed:', redisError);
+ const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`;
+ const cachedSvg = await redis.get(cacheKey);
+ if (cachedSvg) {
+ this.setResponseHeaders(response);
+ return response.send(cachedSvg);
}
const initials = this.getInitials(name);
@@ -49,85 +29,41 @@ export default class AvatarController {
const svgContent = this.createSvg(size, colors, initials);
// // Cache the generated avatar for future use, e.g. 1 hour expiry
- try {
- await redis.setex(cacheKey, CACHE_TTL, svgContent);
- } catch (redisError) {
- // Log but don't fail the request
- console.warn('Redis cache write failed:', redisError);
- }
+ await redis.setex(cacheKey, 3600, svgContent);
this.setResponseHeaders(response);
return response.send(svgContent);
} catch (error) {
- console.error('Avatar generation error:', error);
- return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
- error: 'Failed to generate avatar',
- });
+ return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ error: error.message });
}
}
- private validateSize(size: any): { isValid: boolean; value?: number; error?: string } {
- const numSize = Number(size);
-
- if (isNaN(numSize)) {
- return { isValid: false, error: 'Size must be a valid number' };
- }
-
- if (numSize < MIN_SIZE || numSize > MAX_SIZE) {
- return {
- isValid: false,
- error: `Size must be between ${MIN_SIZE} and ${MAX_SIZE}`,
- };
- }
-
- return { isValid: true, value: Math.floor(numSize) };
- }
-
- private sanitizeName(name: string): string {
- return name
- .trim()
- .toLowerCase()
- .replace(/[^a-z0-9\s-]/gi, '');
- }
-
private getInitials(name: string): string {
- const sanitized = name.trim().replace(/\s+/g, ' '); // normalize whitespace
- const parts = sanitized
+ const parts = name
+ .trim()
.split(' ')
- .filter((part) => part.length > 0)
- .map((part) => part.trim());
+ .filter((part) => part.length > 0);
if (parts.length === 0) {
return 'NA';
}
- if (parts.length === 1) {
- // For single word, take first 2 characters or first char if only 1 char
- return parts[0].substring(0, Math.min(2, parts[0].length)).toUpperCase();
+ if (parts.length >= 2) {
+ return this.getMultiWordInitials(parts);
}
-
- return this.getMultiWordInitials(parts);
+ return parts[0].substring(0, 2).toUpperCase();
}
private getMultiWordInitials(parts: string[]): string {
- // Filter out prefixes and short words
- const significantParts = parts.filter((part) => !PREFIXES.includes(part.toLowerCase()) && part.length > 1);
+ const firstName = parts[0];
+ const lastName = parts[parts.length - 1];
+ const firstInitial = firstName.charAt(0).toUpperCase();
+ const lastInitial = lastName.charAt(0).toUpperCase();
- if (significantParts.length === 0) {
- // Fallback to first and last regardless of prefixes
- const firstName = parts[0];
- const lastName = parts[parts.length - 1];
- return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase();
+ if (PREFIXES.includes(lastName.toLowerCase()) && lastName === lastName.toUpperCase()) {
+ return firstInitial + lastName.charAt(1).toUpperCase();
}
-
- if (significantParts.length === 1) {
- return significantParts[0].substring(0, 2).toUpperCase();
- }
-
- // Take first and last significant parts
- const firstName = significantParts[0];
- const lastName = significantParts[significantParts.length - 1];
- return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase();
+ return firstInitial + lastInitial;
}
private generateColors(name: string): { background: string; text: string } {
@@ -139,44 +75,31 @@ export default class AvatarController {
}
private createSvg(size: number, colors: { background: string; text: string }, initials: string): string {
- const fontSize = Math.max(12, Math.floor(size * FONT_SIZE_RATIO)); // Ensure readable font size
-
- // Escape any potential HTML/XML characters in initials
- const escapedInitials = this.escapeXml(initials);
-
- return ``;
- }
-
- private escapeXml(text: string): string {
- return text.replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, ''');
+ const fontSize = size * FONT_SIZE_RATIO;
+ return `
+
+ `;
}
private setResponseHeaders(response: HttpContext['response']): void {
- response.header('Content-Type', 'image/svg+xml');
- response.header('Cache-Control', 'public, max-age=86400'); // Cache for 1 day
- response.header('ETag', `"${Date.now()}"`); // Simple ETag
+ response.header('Content-type', 'image/svg+xml');
+ response.header('Cache-Control', 'no-cache');
+ response.header('Pragma', 'no-cache');
+ response.header('Expires', '0');
}
private getColorFromName(name: string): string {
let hash = 0;
- const normalizedName = name.toLowerCase().trim();
-
- for (let i = 0; i < normalizedName.length; i++) {
- hash = normalizedName.charCodeAt(i) + ((hash << 5) - hash);
- hash = hash & hash; // Convert to 32-bit integer
+ for (let i = 0; i < name.length; i++) {
+ hash = name.charCodeAt(i) + ((hash << 5) - hash);
}
- // Ensure we get vibrant colors by constraining the color space
const colorParts = [];
for (let i = 0; i < 3; i++) {
- let value = (hash >> (i * 8)) & 0xff;
- // Ensure minimum color intensity for better contrast
- value = Math.max(50, value);
+ const value = (hash >> (i * 8)) & 0xff;
colorParts.push(value.toString(16).padStart(2, '0'));
}
return colorParts.join('');
@@ -187,7 +110,7 @@ export default class AvatarController {
const g = parseInt(hexColor.substring(2, 4), 16);
const b = parseInt(hexColor.substring(4, 6), 16);
- const lightenValue = (value: number) => Math.min(255, Math.floor(value + (255 - value) * (percent / 100)));
+ const lightenValue = (value: number) => Math.min(255, Math.floor((value * (100 + percent)) / 100));
const newR = lightenValue(r);
const newG = lightenValue(g);
@@ -201,7 +124,7 @@ export default class AvatarController {
const g = parseInt(hexColor.slice(2, 4), 16);
const b = parseInt(hexColor.slice(4, 6), 16);
- const darkenValue = (value: number) => Math.max(0, Math.floor(value * COLOR_DARKENING_FACTOR));
+ const darkenValue = (value: number) => Math.round(value * COLOR_DARKENING_FACTOR);
const darkerR = darkenValue(r);
const darkerG = darkenValue(g);
diff --git a/app/Controllers/Http/Api/DatasetController.ts b/app/Controllers/Http/Api/DatasetController.ts
index 9106521..b80949d 100644
--- a/app/Controllers/Http/Api/DatasetController.ts
+++ b/app/Controllers/Http/Api/DatasetController.ts
@@ -1,36 +1,24 @@
import type { HttpContext } from '@adonisjs/core/http';
+// import Person from 'App/Models/Person';
import Dataset from '#models/dataset';
import { StatusCodes } from 'http-status-codes';
-import DatasetReference from '#models/dataset_reference';
// node ace make:controller Author
export default class DatasetController {
- /**
- * GET /api/datasets
- * Find all published datasets
- */
- public async index({ response }: HttpContext) {
- try {
- const datasets = await Dataset.query()
- .where(function (query) {
- query.where('server_state', 'published').orWhere('server_state', 'deleted');
- })
- .preload('titles')
- .preload('identifier')
- .orderBy('server_date_published', 'desc');
+ public async index({}: HttpContext) {
+ // Select datasets with server_state 'published' or 'deleted' and sort by the last published date
+ const datasets = await Dataset.query()
+ .where(function (query) {
+ query.where('server_state', 'published')
+ .orWhere('server_state', 'deleted');
+ })
+ .preload('titles')
+ .preload('identifier')
+ .orderBy('server_date_published', 'desc');
- return response.status(StatusCodes.OK).json(datasets);
- } catch (error) {
- return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
- message: error.message || 'Some error occurred while retrieving datasets.',
- });
- }
+ return datasets;
}
- /**
- * GET /api/dataset
- * Find all published datasets
- */
public async findAll({ response }: HttpContext) {
try {
const datasets = await Dataset.query()
@@ -46,279 +34,34 @@ export default class DatasetController {
}
}
- /**
- * GET /api/dataset/:publish_id
- * Find one dataset by publish_id
- */
- public async findOne({ response, params }: HttpContext) {
- try {
- const dataset = await Dataset.query()
- .where('publish_id', params.publish_id)
- .preload('titles')
- .preload('descriptions') // Using 'descriptions' instead of 'abstracts'
- .preload('user', (builder) => {
- builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']);
- })
- .preload('authors', (builder) => {
- builder
- .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
- .withCount('datasets', (query) => {
- query.as('datasets_count');
- })
- .pivotColumns(['role', 'sort_order'])
- .orderBy('pivot_sort_order', 'asc');
- })
- .preload('contributors', (builder) => {
- builder
- .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
- .withCount('datasets', (query) => {
- query.as('datasets_count');
- })
- .pivotColumns(['role', 'sort_order', 'contributor_type'])
- .orderBy('pivot_sort_order', 'asc');
- })
- .preload('subjects')
- .preload('coverage')
- .preload('licenses')
- .preload('references')
- .preload('project')
- // .preload('referenced_by', (builder) => {
- // builder.preload('dataset', (builder) => {
- // builder.preload('identifier');
- // });
- // })
- .preload('files', (builder) => {
- builder.preload('hashvalues');
- })
- .preload('identifier')
- .first(); // Use first() instead of firstOrFail() to handle not found gracefully
-
- if (!dataset) {
- return response.status(StatusCodes.NOT_FOUND).json({
- message: `Cannot find Dataset with publish_id=${params.publish_id}.`,
+ public async findOne({ params }: HttpContext) {
+ const datasets = await Dataset.query()
+ .where('publish_id', params.publish_id)
+ .preload('titles')
+ .preload('descriptions')
+ .preload('user')
+ .preload('authors', (builder) => {
+ builder.orderBy('pivot_sort_order', 'asc');
+ })
+ .preload('contributors', (builder) => {
+ builder.orderBy('pivot_sort_order', 'asc');
+ })
+ .preload('subjects')
+ .preload('coverage')
+ .preload('licenses')
+ .preload('references')
+ .preload('project')
+ .preload('referenced_by', (builder) => {
+ builder.preload('dataset', (builder) => {
+ builder.preload('identifier');
});
- }
+ })
+ .preload('files', (builder) => {
+ builder.preload('hashvalues');
+ })
+ .preload('identifier')
+ .firstOrFail();
- // Build the version chain
- const versionChain = await this.buildVersionChain(dataset);
-
- // Add version chain to response
- const responseData = {
- ...dataset.toJSON(),
- versionChain: versionChain,
- };
-
- // return response.status(StatusCodes.OK).json(dataset);
- return response.status(StatusCodes.OK).json(responseData);
- } catch (error) {
- return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
- message: error.message || `Error retrieving Dataset with publish_id=${params.publish_id}.`,
- });
- }
- }
-
- /**
- * GET /:prefix/:value
- * Find dataset by identifier (e.g., https://doi.tethys.at/10.24341/tethys.99.2)
- */
- public async findByIdentifier({ response, params }: HttpContext) {
- const identifierValue = `${params.prefix}/${params.value}`;
-
- // Optional: Validate DOI format
- if (!identifierValue.match(/^10\.\d+\/[a-zA-Z0-9._-]+\.[0-9]+(?:\.[0-9]+)*$/)) {
- return response.status(StatusCodes.BAD_REQUEST).json({
- message: `Invalid DOI format: ${identifierValue}`,
- });
- }
-
- try {
- // Method 1: Using subquery with whereIn (most similar to your original)
- const dataset = await Dataset.query()
- // .whereIn('id', (subQuery) => {
- // subQuery.select('dataset_id').from('dataset_identifiers').where('value', identifierValue);
- // })
- .whereHas('identifier', (builder) => {
- builder.where('value', identifierValue);
- })
- .preload('titles')
- .preload('descriptions') // Using 'descriptions' instead of 'abstracts'
- .preload('user', (builder) => {
- builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']);
- })
- .preload('authors', (builder) => {
- builder
- .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
- .withCount('datasets', (query) => {
- query.as('datasets_count');
- })
- .pivotColumns(['role', 'sort_order'])
- .wherePivot('role', 'author')
- .orderBy('pivot_sort_order', 'asc');
- })
- .preload('contributors', (builder) => {
- builder
- .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
- .withCount('datasets', (query) => {
- query.as('datasets_count');
- })
- .pivotColumns(['role', 'sort_order', 'contributor_type'])
- .wherePivot('role', 'contributor')
- .orderBy('pivot_sort_order', 'asc');
- })
- .preload('subjects')
- .preload('coverage')
- .preload('licenses')
- .preload('references')
- .preload('project')
- // .preload('referenced_by', (builder) => {
- // builder.preload('dataset', (builder) => {
- // builder.preload('identifier');
- // });
- // })
- .preload('files', (builder) => {
- builder.preload('hashvalues');
- })
- .preload('identifier')
- .first();
-
- if (!dataset) {
- return response.status(StatusCodes.NOT_FOUND).json({
- message: `Cannot find Dataset with identifier=${identifierValue}.`,
- });
- }
- // Build the version chain
- const versionChain = await this.buildVersionChain(dataset);
-
- // Add version chain to response
- const responseData = {
- ...dataset.toJSON(),
- versionChain: versionChain,
- };
-
- // return response.status(StatusCodes.OK).json(dataset);
- return response.status(StatusCodes.OK).json(responseData);
- } catch (error) {
- return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
- message: error.message || `Error retrieving Dataset with identifier=${identifierValue}.`,
- });
- }
- }
-
- /**
- * Build the complete version chain for a dataset
- * Traverses both backwards (previous versions) and forwards (newer versions)
- */
- private async buildVersionChain(dataset: Dataset) {
- const versionChain = {
- current: {
- id: dataset.id,
- publish_id: dataset.publish_id,
- doi: dataset.identifier?.value || null,
- main_title: dataset.mainTitle || null,
- server_date_published: dataset.server_date_published,
- },
- previousVersions: [] as any[],
- newerVersions: [] as any[],
- };
-
- // Get all previous versions (going backwards in time)
- versionChain.previousVersions = await this.getPreviousVersions(dataset.id);
-
- // Get all newer versions (going forwards in time)
- versionChain.newerVersions = await this.getNewerVersions(dataset.id);
-
- return versionChain;
- }
-
- /**
- * Recursively get all previous versions
- */
- private async getPreviousVersions(datasetId: number, visited: Set = new Set()): Promise {
- // Prevent infinite loops
- if (visited.has(datasetId)) {
- return [];
- }
- visited.add(datasetId);
-
- const previousVersions: any[] = [];
-
- // Find references where this dataset "IsNewVersionOf" another dataset
- const previousRefs = await DatasetReference.query()
- .where('document_id', datasetId)
- .where('relation', 'IsNewVersionOf')
- .whereNotNull('related_document_id');
-
- for (const ref of previousRefs) {
- if (!ref.related_document_id) continue;
-
- const previousDataset = await Dataset.query()
- .where('id', ref.related_document_id)
- .preload('identifier')
- .preload('titles')
- .first();
-
- if (previousDataset) {
- const versionInfo = {
- id: previousDataset.id,
- publish_id: previousDataset.publish_id,
- doi: previousDataset.identifier?.value || null,
- main_title: previousDataset.mainTitle || null,
- server_date_published: previousDataset.server_date_published,
- relation: 'IsPreviousVersionOf', // From perspective of current dataset
- };
-
- previousVersions.push(versionInfo);
-
- // Recursively get even older versions
- const olderVersions = await this.getPreviousVersions(previousDataset.id, visited);
- previousVersions.push(...olderVersions);
- }
- }
-
- return previousVersions;
- }
-
- /**
- * Recursively get all newer versions
- */
- private async getNewerVersions(datasetId: number, visited: Set = new Set()): Promise {
- // Prevent infinite loops
- if (visited.has(datasetId)) {
- return [];
- }
- visited.add(datasetId);
-
- const newerVersions: any[] = [];
-
- // Find references where this dataset "IsPreviousVersionOf" another dataset
- const newerRefs = await DatasetReference.query()
- .where('document_id', datasetId)
- .where('relation', 'IsPreviousVersionOf')
- .whereNotNull('related_document_id');
-
- for (const ref of newerRefs) {
- if (!ref.related_document_id) continue;
-
- const newerDataset = await Dataset.query().where('id', ref.related_document_id).preload('identifier').preload('titles').first();
-
- if (newerDataset) {
- const versionInfo = {
- id: newerDataset.id,
- publish_id: newerDataset.publish_id,
- doi: newerDataset.identifier?.value || null,
- main_title: newerDataset.mainTitle || null,
- server_date_published: newerDataset.server_date_published,
- relation: 'IsNewVersionOf', // From perspective of current dataset
- };
-
- newerVersions.push(versionInfo);
-
- // Recursively get even newer versions
- const evenNewerVersions = await this.getNewerVersions(newerDataset.id, visited);
- newerVersions.push(...evenNewerVersions);
- }
- }
-
- return newerVersions;
+ return datasets;
}
}
diff --git a/app/Controllers/Http/Api/FileController.ts b/app/Controllers/Http/Api/FileController.ts
index 8a400ad..8080479 100644
--- a/app/Controllers/Http/Api/FileController.ts
+++ b/app/Controllers/Http/Api/FileController.ts
@@ -2,103 +2,53 @@ import type { HttpContext } from '@adonisjs/core/http';
import File from '#models/file';
import { StatusCodes } from 'http-status-codes';
import * as fs from 'fs';
-import { DateTime } from 'luxon';
+import * as path from 'path';
// node ace make:controller Author
export default class FileController {
// @Get("download/:id")
public async findOne({ response, params }: HttpContext) {
const id = params.id;
- // const file = await File.findOrFail(id);
- // Load file with its related dataset to check embargo
- const file = await File.query()
- .where('id', id)
- .preload('dataset') // or 'dataset' - whatever your relationship is named
- .firstOrFail();
+ const file = await File.findOrFail(id);
+ // const file = await File.findOne({
+ // where: { id: id },
+ // });
+ if (file) {
+ const filePath = '/storage/app/data/' + file.pathName;
+ const ext = path.extname(filePath);
+ const fileName = file.label + ext;
+ try {
+ fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
+ // console.log("can read/write:", path);
+
+ response
+ .header('Cache-Control', 'no-cache private')
+ .header('Content-Description', 'File Transfer')
+ .header('Content-Type', file.mimeType)
+ .header('Content-Disposition', 'inline; filename=' + fileName)
+ .header('Content-Transfer-Encoding', 'binary')
+ .header('Access-Control-Allow-Origin', '*')
+ .header('Access-Control-Allow-Methods', 'GET,POST');
+
+ response.status(StatusCodes.OK).download(filePath);
+ } catch (err) {
+ // console.log("no access:", path);
+ response.status(StatusCodes.NOT_FOUND).send({
+ message: `File with id ${id} doesn't exist on file server`,
+ });
+ }
- if (!file) {
- return response.status(StatusCodes.NOT_FOUND).send({
+ // res.status(StatusCodes.OK).sendFile(filePath, (err) => {
+ // // res.setHeader("Content-Type", "application/json");
+ // // res.removeHeader("Content-Disposition");
+ // res.status(StatusCodes.NOT_FOUND).send({
+ // message: `File with id ${id} doesn't exist on file server`,
+ // });
+ // });
+ } else {
+ response.status(StatusCodes.NOT_FOUND).send({
message: `Cannot find File with id=${id}.`,
});
}
-
- const dataset = file.dataset;
- // Files from unpublished datasets are now blocked
- if (dataset.server_state !== 'published') {
- return response.status(StatusCodes.FORBIDDEN).send({
- message: `File access denied: Dataset is not published.`,
- });
- }
- if (dataset && this.isUnderEmbargo(dataset.embargo_date)) {
- return response.status(StatusCodes.FORBIDDEN).send({
- message: `File is under embargo until ${dataset.embargo_date?.toFormat('yyyy-MM-dd')}`,
- });
- }
-
- // Proceed with file download
- const filePath = '/storage/app/data/' + file.pathName;
- const fileExt = file.filePath.split('.').pop() || '';
- // const fileName = file.label + fileExt;
- const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
-
- // Determine if file can be previewed inline in browser
- const canPreviewInline = (mimeType: string): boolean => {
- const type = mimeType.toLowerCase();
- return (
- type === 'application/pdf' ||
- type.startsWith('image/') ||
- type.startsWith('text/') ||
- type === 'application/json' ||
- type === 'application/xml' ||
- // Uncomment if you want video/audio inline
- type.startsWith('video/') ||
- type.startsWith('audio/')
- );
- };
- const disposition = canPreviewInline(file.mimeType) ? 'inline' : 'attachment';
-
- try {
- fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
- // console.log("can read/write:", filePath);
-
- response
- .header('Cache-Control', 'no-cache private')
- .header('Content-Description', 'File Transfer')
- .header('Content-Type', file.mimeType)
- .header('Content-Disposition', `${disposition}; filename="${fileName}"`)
- .header('Content-Transfer-Encoding', 'binary')
- .header('Access-Control-Allow-Origin', '*')
- .header('Access-Control-Allow-Methods', 'GET');
-
- response.status(StatusCodes.OK).download(filePath);
- } catch (err) {
- // console.log("no access:", path);
- response.status(StatusCodes.NOT_FOUND).send({
- message: `File with id ${id} doesn't exist on file server`,
- });
- }
- }
-
- /**
- * Check if the dataset is under embargo
- * Compares only dates (ignoring time) for embargo check
- * @param embargoDate - The embargo date from dataset
- * @returns true if under embargo, false if embargo has passed or no embargo set
- */
- private isUnderEmbargo(embargoDate: DateTime | null): boolean {
- // No embargo date set - allow download
- if (!embargoDate) {
- return false;
- }
-
- // Get current date at start of day (00:00:00)
- const today = DateTime.now().startOf('day');
-
- // Get embargo date at start of day (00:00:00)
- const embargoDateOnly = embargoDate.startOf('day');
-
- // File is under embargo if embargo date is after today
- // This means the embargo lifts at the start of the embargo date
- return embargoDateOnly >= today;
}
}
diff --git a/app/Controllers/Http/Editor/DatasetController.ts b/app/Controllers/Http/Editor/DatasetController.ts
index f2a0417..5ec3910 100644
--- a/app/Controllers/Http/Editor/DatasetController.ts
+++ b/app/Controllers/Http/Editor/DatasetController.ts
@@ -3,7 +3,7 @@ import { Client } from '@opensearch-project/opensearch';
import User from '#models/user';
import Dataset from '#models/dataset';
import DatasetIdentifier from '#models/dataset_identifier';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import { create } from 'xmlbuilder2';
import { readFileSync } from 'fs';
@@ -188,16 +188,10 @@ export default class DatasetsController {
}
}
- public async approve({ request, inertia, response, auth }: HttpContext) {
+ public async approve({ request, inertia, response }: HttpContext) {
const id = request.param('id');
-
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
// $dataset = Dataset::with('user:id,login')->findOrFail($id);
- const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).firstOrFail();
+ const dataset = await Dataset.findOrFail(id);
const validStates = ['editor_accepted', 'rejected_reviewer'];
if (!validStates.includes(dataset.server_state)) {
@@ -223,7 +217,7 @@ export default class DatasetsController {
});
}
- public async approveUpdate({ request, response, auth }: HttpContext) {
+ public async approveUpdate({ request, response }: HttpContext) {
const approveDatasetSchema = vine.object({
reviewer_id: vine.number(),
});
@@ -236,11 +230,7 @@ export default class DatasetsController {
throw error;
}
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
- const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).firstOrFail();
+ const dataset = await Dataset.findOrFail(id);
const validStates = ['editor_accepted', 'rejected_reviewer'];
if (!validStates.includes(dataset.server_state)) {
@@ -262,6 +252,7 @@ export default class DatasetsController {
dataset.reject_editor_note = null;
}
+
//save main and additional titles
const reviewer_id = request.input('reviewer_id', null);
dataset.reviewer_id = reviewer_id;
@@ -271,15 +262,10 @@ export default class DatasetsController {
}
}
- public async reject({ request, inertia, response, auth }: HttpContext) {
+ public async reject({ request, inertia, response }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
const dataset = await Dataset.query()
.where('id', id)
- .where('editor_id', user.id) // Ensure the user is the editor of the dataset
// .preload('titles')
// .preload('descriptions')
.preload('user', (builder) => {
@@ -304,17 +290,14 @@ export default class DatasetsController {
});
}
+
+
public async rejectUpdate({ request, response, auth }: HttpContext) {
const authUser = auth.user!;
-
- if (!authUser) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
const id = request.param('id');
const dataset = await Dataset.query()
.where('id', id)
- .where('editor_id', authUser.id) // Ensure the user is the editor of the dataset
.preload('user', (builder) => {
builder.select('id', 'login', 'email');
})
@@ -397,14 +380,9 @@ export default class DatasetsController {
public async publish({ request, inertia, response, auth }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
const dataset = await Dataset.query()
.where('id', id)
- .where('editor_id', user.id) // Ensure the user is the editor of the dataset
.preload('titles')
.preload('authors')
// .preload('persons', (builder) => {
@@ -424,16 +402,18 @@ export default class DatasetsController {
.back();
}
+
+
return inertia.render('Editor/Dataset/Publish', {
dataset,
- can: {
- reject: await auth.user?.can(['dataset-editor-reject']),
+ can: {
+ reject: await auth.user?.can(['dataset-editor-reject']),
publish: await auth.user?.can(['dataset-publish']),
},
});
}
- public async publishUpdate({ request, response, auth }: HttpContext) {
+ public async publishUpdate({ request, response }: HttpContext) {
const publishDatasetSchema = vine.object({
publisher_name: vine.string().trim(),
});
@@ -445,12 +425,7 @@ export default class DatasetsController {
throw error;
}
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).firstOrFail();
+ const dataset = await Dataset.findOrFail(id);
// let test = await Dataset.getMax('publish_id');
// const maxPublishId = await Database.from('documents').max('publish_id as max_publish_id').first();
@@ -476,16 +451,10 @@ export default class DatasetsController {
}
}
- public async rejectToReviewer({ request, inertia, response, auth }: HttpContext) {
+ public async rejectToReviewer({ request, inertia, response }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
const dataset = await Dataset.query()
- .where('id', id)
- .where('editor_id', user.id) // Ensure the user is the editor of the dataset
+ .where('id', id)
.preload('reviewer', (builder) => {
builder.select('id', 'login', 'email');
})
@@ -511,14 +480,9 @@ export default class DatasetsController {
public async rejectToReviewerUpdate({ request, response, auth }: HttpContext) {
const authUser = auth.user!;
- if (!authUser) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
const id = request.param('id');
const dataset = await Dataset.query()
.where('id', id)
- .where('editor_id', authUser.id) // Ensure the user is the editor of the dataset
.preload('reviewer', (builder) => {
builder.select('id', 'login', 'email');
})
@@ -591,6 +555,7 @@ export default class DatasetsController {
}
}
+
return response
.flash(
`You have successfully rejected dataset ${dataset.id} reviewed by ${dataset.reviewer.login}.${emailStatusMessage}`,
@@ -599,16 +564,10 @@ export default class DatasetsController {
.toRoute('editor.dataset.list');
}
- public async doiCreate({ request, inertia, auth, response }: HttpContext) {
+ public async doiCreate({ request, inertia }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
const dataset = await Dataset.query()
.where('id', id)
- .where('editor_id', user.id) // Ensure the user is the editor of the dataset
.preload('titles')
.preload('descriptions')
// .preload('identifier')
@@ -619,110 +578,60 @@ export default class DatasetsController {
});
}
- public async doiStore({ request, response, auth }: HttpContext) {
+ public async doiStore({ request, response }: HttpContext) {
const dataId = request.param('publish_id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- // Load dataset with minimal required relationships
const dataset = await Dataset.query()
- .where('editor_id', user.id) // Ensure the user is the editor of the dataset
+ // .preload('xmlCache')
.where('publish_id', dataId)
.firstOrFail();
-
- const prefix = process.env.DATACITE_PREFIX || '';
- const base_domain = process.env.BASE_DOMAIN || '';
-
- // Generate DOI metadata XML
const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
- // Prepare DOI registration data
- const doiValue = `${prefix}/tethys.${dataset.publish_id}`; //'10.21388/tethys.213'
- const landingPageUrl = `https://doi.${getDomain(base_domain)}/${prefix}/tethys.${dataset.publish_id}`; //https://doi.dev.tethys.at/10.21388/tethys.213
+ let prefix = '';
+ let base_domain = '';
+ // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
+ prefix = process.env.DATACITE_PREFIX || '';
+ base_domain = process.env.BASE_DOMAIN || '';
- // Register DOI with DataCite
+ // register DOI:
+ const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213'
+ const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213
const doiClient = new DoiClient();
const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);
- if (dataciteResponse?.status !== 201) {
+ if (dataciteResponse?.status === 201) {
+ // if response OK 201; save the Identifier value into db
+ const doiIdentifier = new DatasetIdentifier();
+ doiIdentifier.value = doiValue;
+ doiIdentifier.dataset_id = dataset.id;
+ doiIdentifier.type = 'doi';
+ doiIdentifier.status = 'findable';
+ // save modified date of datset for re-caching model in db an update the search index
+ dataset.server_date_modified = DateTime.now();
+
+ // save updated dataset to db an index to OpenSearch
+ try {
+ await dataset.related('identifier').save(doiIdentifier);
+ const index_name = 'tethys-records';
+ await Index.indexDocument(dataset, index_name);
+ } catch (error) {
+ logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`);
+ // Log the error or handle it as needed
+ throw new HttpException(error.message);
+ }
+ return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
+ } else {
const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`;
+ // Log the error or handle it as needed
throw new DoiClientException(dataciteResponse?.status, message);
}
-
- // DOI registration successful - persist and index
- try {
- // Save identifier
- await this.persistDoiAndIndex(dataset, doiValue);
-
- return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
- } catch (error) {
- logger.error(`${__filename}: Failed to persist DOI and index dataset ${dataset.id}: ${error.message}`);
- throw new HttpException(error.message);
- }
-
// return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
}
- /**
- * Persist DOI identifier and update search index
- * Handles cache invalidation to ensure fresh indexing
- */
- private async persistDoiAndIndex(dataset: Dataset, doiValue: string): Promise {
- // Create DOI identifier
- const doiIdentifier = new DatasetIdentifier();
- doiIdentifier.value = doiValue;
- doiIdentifier.dataset_id = dataset.id;
- doiIdentifier.type = 'doi';
- doiIdentifier.status = 'findable';
-
- // Save identifier (this will trigger database insert)
- await dataset.related('identifier').save(doiIdentifier);
-
- // Update dataset modification timestamp to reflect the change
- dataset.server_date_modified = DateTime.now();
- await dataset.save();
-
- // Invalidate stale XML cache
- await this.invalidateDatasetCache(dataset);
-
- // Reload dataset with fresh state for indexing
- const freshDataset = await Dataset.query().where('id', dataset.id).preload('identifier').preload('xmlCache').firstOrFail();
-
- // Index to OpenSearch with fresh data
- const index_name = process.env.OPENSEARCH_INDEX || 'tethys-records';
- await Index.indexDocument(freshDataset, index_name);
-
- logger.info(`Successfully created DOI ${doiValue} and indexed dataset ${dataset.id}`);
- }
-
- /**
- * Invalidate XML cache for dataset
- * Ensures fresh cache generation on next access
- */
- private async invalidateDatasetCache(dataset: Dataset): Promise {
- await dataset.load('xmlCache');
-
- if (dataset.xmlCache) {
- await dataset.xmlCache.delete();
- logger.debug(`Invalidated XML cache for dataset ${dataset.id}`);
- }
- }
-
public async show({}: HttpContext) {}
- public async edit({ request, inertia, response, auth }: HttpContext) {
+ public async edit({ request, inertia, response }: HttpContext) {
const id = request.param('id');
-
- // Check if user is authenticated
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- // Prefilter by both id AND editor_id to ensure user has permission to edit
- const datasetQuery = Dataset.query().where('id', id).where('editor_id', user.id);
+ const datasetQuery = Dataset.query().where('id', id);
datasetQuery
.preload('titles', (query) => query.orderBy('id', 'asc'))
.preload('descriptions', (query) => query.orderBy('id', 'asc'))
@@ -739,7 +648,6 @@ export default class DatasetsController {
query.orderBy('sort_order', 'asc'); // Sort by sort_order column
});
- // This will throw 404 if editor_id does not match logged in user
const dataset = await datasetQuery.firstOrFail();
const validStates = ['editor_accepted', 'rejected_reviewer'];
if (!validStates.includes(dataset.server_state)) {
@@ -813,16 +721,11 @@ export default class DatasetsController {
});
}
- public async update({ request, response, session, auth }: HttpContext) {
+ public async update({ request, response, session }: HttpContext) {
// Get the dataset id from the route parameter
const datasetId = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
// Retrieve the dataset and load its existing files
- const dataset = await Dataset.query().where('id', datasetId).where('editor_id', user.id).firstOrFail();
+ const dataset = await Dataset.findOrFail(datasetId);
await dataset.load('files');
let trx: TransactionClientContract | null = null;
@@ -831,7 +734,7 @@ export default class DatasetsController {
trx = await db.transaction();
// const user = (await User.find(auth.user?.id)) as User;
// await this.createDatasetAndAssociations(user, request, trx);
- // const dataset = await Dataset.findOrFail(datasetId);
+ const dataset = await Dataset.findOrFail(datasetId);
// save the licenses
const licenses: number[] = request.input('licenses', []);
@@ -997,7 +900,6 @@ export default class DatasetsController {
const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']);
// dataset.type = request.input('type');
dataset.merge(input);
- dataset.server_date_modified = DateTime.now();
// let test: boolean = dataset.$isDirty;
await dataset.useTransaction(trx).save();
@@ -1017,15 +919,10 @@ export default class DatasetsController {
}
}
- public async categorize({ inertia, request, response, auth }: HttpContext) {
+ public async categorize({ inertia, request, response }: HttpContext) {
const id = request.param('id');
- // Check if user is authenticated
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
// Preload dataset and its "collections" relation
- const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).preload('collections').firstOrFail();
+ const dataset = await Dataset.query().where('id', id).preload('collections').firstOrFail();
const validStates = ['editor_accepted', 'rejected_reviewer'];
if (!validStates.includes(dataset.server_state)) {
// session.flash('errors', 'Invalid server state!');
@@ -1053,15 +950,10 @@ export default class DatasetsController {
});
}
- public async categorizeUpdate({ request, response, session, auth }: HttpContext) {
+ public async categorizeUpdate({ request, response, session }: HttpContext) {
// Get the dataset id from the route parameter
const id = request.param('id');
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
- // Retrieve the dataset and load its existing files
- const dataset = await Dataset.query().preload('files').where('id', id).where('editor_id', user.id).firstOrFail();
+ const dataset = await Dataset.query().preload('files').where('id', id).firstOrFail();
const validStates = ['editor_accepted', 'rejected_reviewer'];
if (!validStates.includes(dataset.server_state)) {
@@ -1229,20 +1121,9 @@ export default class DatasetsController {
// const filePath = await drive.use('local').getUrl('/'+ file.filePath)
const filePath = file.filePath;
const fileExt = file.filePath.split('.').pop() || '';
-
- // Check if label already includes the extension
- const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
-
// Set the response headers and download the file
- response
- .header('Cache-Control', 'no-cache private')
- .header('Content-Description', 'File Transfer')
- .header('Content-Type', file.mime_type || 'application/octet-stream')
- // .header('Content-Disposition', 'inline; filename=' + fileName)
- .header('Content-Transfer-Encoding', 'binary')
- .header('Access-Control-Allow-Origin', '*')
- .header('Access-Control-Allow-Methods', 'GET');
- response.attachment(fileName);
+ response.header('Content-Type', file.mime_type || 'application/octet-stream');
+ response.attachment(`${file.label}.${fileExt}`);
return response.download(filePath);
}
@@ -1255,18 +1136,19 @@ export default class DatasetsController {
}
}
- private async getDatasetXmlDomNode(dataset: Dataset): Promise {
- const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
+ private async getDatasetXmlDomNode(dataset: Dataset) {
+ const xmlModel = new XmlModel(dataset);
// xmlModel.setModel(dataset);
-
- // Load existing cache if available
- await dataset.load('xmlCache');
+ xmlModel.excludeEmptyFields();
+ xmlModel.caching = true;
+ // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+ // dataset.load('xmlCache');
if (dataset.xmlCache) {
- serializer.setCache(dataset.xmlCache);
+ xmlModel.xmlCache = dataset.xmlCache;
}
// return cache.getDomDocument();
- const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
- return xmlDocument;
+ const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+ return domDocument;
}
}
diff --git a/app/Controllers/Http/Oai/OaiController.ts b/app/Controllers/Http/Oai/OaiController.ts
index 47d1708..db49a32 100644
--- a/app/Controllers/Http/Oai/OaiController.ts
+++ b/app/Controllers/Http/Oai/OaiController.ts
@@ -15,7 +15,7 @@ import { OaiModelException, BadOaiModelException } from '#app/exceptions/OaiMode
import Dataset from '#models/dataset';
import Collection from '#models/collection';
import { getDomain, preg_match } from '#app/utils/utility-functions';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
import logger from '@adonisjs/core/services/logger';
import ResumptionToken from '#app/Library/Oai/ResumptionToken';
// import Config from '@ioc:Adonis/Core/Config';
@@ -292,7 +292,7 @@ export default class OaiController {
this.xsltParameter['repIdentifier'] = repIdentifier;
const datasetNode = this.xml.root().ele('Datasets');
- const paginationParams: PagingParameter = {
+ const paginationParams: PagingParameter ={
cursor: 0,
totalLength: 0,
start: maxRecords + 1,
@@ -333,7 +333,7 @@ export default class OaiController {
}
private async handleNoResumptionToken(oaiRequest: Dictionary, paginationParams: PagingParameter, maxRecords: number) {
- this.validateMetadataPrefix(oaiRequest, paginationParams);
+ this.validateMetadataPrefix(oaiRequest, paginationParams);
const finder: ModelQueryBuilderContract = Dataset.query().whereIn(
'server_state',
this.deliveringDocumentStates,
@@ -347,20 +347,16 @@ export default class OaiController {
finder: ModelQueryBuilderContract,
paginationParams: PagingParameter,
oaiRequest: Dictionary,
- maxRecords: number,
+ maxRecords: number
) {
const totalResult = await finder
.clone()
.count('* as total')
.first()
.then((res) => res?.$extras.total);
- paginationParams.totalLength = Number(totalResult);
+ paginationParams.totalLength = Number(totalResult);
- const combinedRecords: Dataset[] = await finder
- .select('publish_id')
- .orderBy('publish_id')
- .offset(0)
- .limit(maxRecords * 2);
+ const combinedRecords: Dataset[] = await finder.select('publish_id').orderBy('publish_id').offset(0).limit(maxRecords*2);
paginationParams.activeWorkIds = combinedRecords.slice(0, 100).map((dat) => Number(dat.publish_id));
paginationParams.nextDocIds = combinedRecords.slice(100).map((dat) => Number(dat.publish_id));
@@ -606,17 +602,19 @@ export default class OaiController {
}
private async getDatasetXmlDomNode(dataset: Dataset) {
- const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
-
+ const xmlModel = new XmlModel(dataset);
+ // xmlModel.setModel(dataset);
+ xmlModel.excludeEmptyFields();
+ xmlModel.caching = true;
// const cache = dataset.xmlCache ? dataset.xmlCache : null;
// dataset.load('xmlCache');
if (dataset.xmlCache) {
- serializer.setCache(dataset.xmlCache);
+ xmlModel.xmlCache = dataset.xmlCache;
}
- // return cache.toXmlDocument();
- const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
- return xmlDocument;
+ // return cache.getDomDocument();
+ const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+ return domDocument;
}
private addSpecInformation(domNode: XMLBuilder, information: string) {
diff --git a/app/Controllers/Http/Reviewer/DatasetController.ts b/app/Controllers/Http/Reviewer/DatasetController.ts
index 27f9b46..6b54772 100644
--- a/app/Controllers/Http/Reviewer/DatasetController.ts
+++ b/app/Controllers/Http/Reviewer/DatasetController.ts
@@ -107,12 +107,13 @@ export default class DatasetsController {
}
return inertia.render('Reviewer/Dataset/Review', {
- dataset,
+ dataset,
can: {
review: await auth.user?.can(['dataset-review']),
reject: await auth.user?.can(['dataset-review-reject']),
},
});
+
}
public async review_old({ request, inertia, response, auth }: HttpContext) {
@@ -369,19 +370,6 @@ export default class DatasetsController {
.flash(`You have rejected dataset ${dataset.id}! to editor ${dataset.editor.login}`, 'message');
}
- // public async download({ params, response }: HttpContext) {
- // const id = params.id;
- // // Find the file by ID
- // const file = await File.findOrFail(id);
- // // const filePath = await drive.use('local').getUrl('/'+ file.filePath)
- // const filePath = file.filePath;
- // const fileExt = file.filePath.split('.').pop() || '';
- // // Set the response headers and download the file
- // response.header('Content-Type', file.mime_type || 'application/octet-stream');
- // response.attachment(`${file.label}.${fileExt}`);
- // return response.download(filePath);
- // }
-
public async download({ params, response }: HttpContext) {
const id = params.id;
// Find the file by ID
@@ -389,20 +377,9 @@ export default class DatasetsController {
// const filePath = await drive.use('local').getUrl('/'+ file.filePath)
const filePath = file.filePath;
const fileExt = file.filePath.split('.').pop() || '';
-
- // Check if label already includes the extension
- const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
-
// Set the response headers and download the file
- response
- .header('Cache-Control', 'no-cache private')
- .header('Content-Description', 'File Transfer')
- .header('Content-Type', file.mime_type || 'application/octet-stream')
- // .header('Content-Disposition', 'inline; filename=' + fileName)
- .header('Content-Transfer-Encoding', 'binary')
- .header('Access-Control-Allow-Origin', '*')
- .header('Access-Control-Allow-Methods', 'GET');
- response.attachment(fileName);
+ response.header('Content-Type', file.mime_type || 'application/octet-stream');
+ response.attachment(`${file.label}.${fileExt}`);
return response.download(filePath);
}
}
diff --git a/app/Controllers/Http/Submitter/DatasetController.ts b/app/Controllers/Http/Submitter/DatasetController.ts
index d666e6f..245b5d9 100644
--- a/app/Controllers/Http/Submitter/DatasetController.ts
+++ b/app/Controllers/Http/Submitter/DatasetController.ts
@@ -105,7 +105,6 @@ export default class DatasetController {
'reviewed',
'rejected_editor',
'rejected_reviewer',
- 'rejected_to_reviewer',
])
.where('account_id', user.id)
.preload('titles')
@@ -234,9 +233,8 @@ export default class DatasetController {
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.minLength(1)
@@ -251,9 +249,8 @@ export default class DatasetController {
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
}),
)
@@ -327,9 +324,8 @@ export default class DatasetController {
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.minLength(1)
@@ -344,9 +340,8 @@ export default class DatasetController {
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
}),
)
@@ -824,20 +819,13 @@ export default class DatasetController {
};
// public async release({ params, view }) {
- public async release({ request, inertia, response, auth }: HttpContext) {
+ public async release({ request, inertia, response }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
-
- // Check if user is authenticated
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
const dataset = await Dataset.query()
.preload('user', (builder) => {
builder.select('id', 'login');
})
- .where('account_id', user.id) // Only fetch if user owns it
.where('id', id)
.firstOrFail();
@@ -858,20 +846,9 @@ export default class DatasetController {
});
}
- public async releaseUpdate({ request, response, auth }: HttpContext) {
+ public async releaseUpdate({ request, response }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
-
- // Check if user is authenticated
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- const dataset = await Dataset.query()
- .preload('files')
- .where('id', id)
- .where('account_id', user.id) // Only fetch if user owns it
- .firstOrFail();
+ const dataset = await Dataset.query().preload('files').where('id', id).firstOrFail();
const validStates = ['inprogress', 'rejected_editor'];
if (!validStates.includes(dataset.server_state)) {
@@ -951,15 +928,7 @@ export default class DatasetController {
public async edit({ request, inertia, response, auth }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
-
- // Check if user is authenticated
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- // Prefilter by both id AND account_id
- const datasetQuery = Dataset.query().where('id', id).where('account_id', user.id); // Only fetch if user owns it
+ const datasetQuery = Dataset.query().where('id', id);
datasetQuery
.preload('titles', (query) => query.orderBy('id', 'asc'))
.preload('descriptions', (query) => query.orderBy('id', 'asc'))
@@ -975,9 +944,8 @@ export default class DatasetController {
.preload('files', (query) => {
query.orderBy('sort_order', 'asc'); // Sort by sort_order column
});
- // This will throw 404 if dataset doesn't exist OR user doesn't own it
- const dataset = await datasetQuery.firstOrFail();
+ const dataset = await datasetQuery.firstOrFail();
const validStates = ['inprogress', 'rejected_editor'];
if (!validStates.includes(dataset.server_state)) {
// session.flash('errors', 'Invalid server state!');
@@ -1015,6 +983,19 @@ export default class DatasetController {
const years = Array.from({ length: currentYear - 1990 + 1 }, (_, index) => 1990 + index);
const licenses = await License.query().select('id', 'name_long').where('active', 'true').pluck('name_long', 'id');
+ // const userHasRoles = user.roles;
+ // const datasetHasLicenses = await dataset.related('licenses').query().pluck('id');
+ // const checkeds = dataset.licenses.first().id;
+
+ // const doctypes = {
+ // analysisdata: { label: 'Analysis', value: 'analysisdata' },
+ // measurementdata: { label: 'Measurements', value: 'measurementdata' },
+ // monitoring: 'Monitoring',
+ // remotesensing: 'Remote Sensing',
+ // gis: 'GIS',
+ // models: 'Models',
+ // mixedtype: 'Mixed Type',
+ // };
return inertia.render('Submitter/Dataset/Edit', {
dataset,
@@ -1034,37 +1015,18 @@ export default class DatasetController {
referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })),
relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })),
doctypes: DatasetTypes,
- can: {
+ can: {
edit: await auth.user?.can(['dataset-edit']),
delete: await auth.user?.can(['dataset-delete']),
},
});
}
- public async update({ request, response, session, auth }: HttpContext) {
+ public async update({ request, response, session }: HttpContext) {
// Get the dataset id from the route parameter
const datasetId = request.param('id');
- const user = auth.user;
-
- // Check if user is authenticated
- if (!user) {
- return response.flash('You must be logged in to update a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- // Prefilter by both id AND account_id
- const dataset = await Dataset.query()
- .where('id', datasetId)
- .where('account_id', user.id) // Only fetch if user owns it
- .firstOrFail();
-
- // // Check if the authenticated user is the owner of the dataset
- // if (dataset.account_id !== user.id) {
- // return response
- // .flash(`Unauthorized access. You are not the owner of dataset with id ${id}.`, 'error')
- // .redirect()
- // .toRoute('dataset.list');
- // }
-
+ // Retrieve the dataset and load its existing files
+ const dataset = await Dataset.findOrFail(datasetId);
await dataset.load('files');
// Accumulate the size of the already related files
// const preExistingFileSize = dataset.files.reduce((acc, file) => acc + file.fileSize, 0);
@@ -1201,93 +1163,42 @@ export default class DatasetController {
}
}
- // ============================================
- // IMPROVED SUBJECTS PROCESSING
- // ============================================
- const subjects = request.input('subjects', []);
- const currentDatasetSubjectIds = new Set();
-
+ // Process all subjects/keywords from the request
+ const subjects = request.input('subjects');
for (const subjectData of subjects) {
- let subjectToRelate: Subject;
-
- // Case 1: Subject has an ID (existing subject being updated)
+ // Case 1: Subject already exists in the database (has an ID)
if (subjectData.id) {
+ // Retrieve the existing subject
const existingSubject = await Subject.findOrFail(subjectData.id);
- // Check if the updated value conflicts with another existing subject
- const duplicateSubject = await Subject.query()
- .where('value', subjectData.value)
- .where('type', subjectData.type)
- .where('language', subjectData.language || 'en') // Default language if not provided
- .where('id', '!=', subjectData.id) // Exclude the current subject
- .first();
+ // Update subject properties from the request data
+ existingSubject.value = subjectData.value;
+ existingSubject.type = subjectData.type;
+ existingSubject.external_key = subjectData.external_key;
- if (duplicateSubject) {
- // A duplicate exists - use the existing duplicate instead
- subjectToRelate = duplicateSubject;
-
- // Check if the original subject should be deleted (if it's only used by this dataset)
- const originalSubjectUsage = await Subject.query()
- .where('id', existingSubject.id)
- .withCount('datasets')
- .firstOrFail();
-
- if (originalSubjectUsage.$extras.datasets_count <= 1) {
- // Only used by this dataset, safe to delete after detaching
- await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]);
- await existingSubject.useTransaction(trx).delete();
- } else {
- // Used by other datasets, just detach from this one
- await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]);
- }
- } else {
- // No duplicate found, update the existing subject
- existingSubject.value = subjectData.value;
- existingSubject.type = subjectData.type;
- existingSubject.language = subjectData.language;
- existingSubject.external_key = subjectData.external_key;
-
- if (existingSubject.$isDirty) {
- await existingSubject.useTransaction(trx).save();
- }
-
- subjectToRelate = existingSubject;
+ // Only save if there are actual changes
+ if (existingSubject.$isDirty) {
+ await existingSubject.save();
}
+
+ // Note: The relationship between dataset and subject is already established,
+ // so we don't need to attach it again
}
// Case 2: New subject being added (no ID)
else {
- // Use firstOrNew to either find existing or create new subject
- subjectToRelate = await Subject.firstOrNew(
- {
- value: subjectData.value,
- type: subjectData.type,
- language: subjectData.language || 'en',
- },
- {
- value: subjectData.value,
- type: subjectData.type,
- language: subjectData.language || 'en',
- external_key: subjectData.external_key,
- },
- );
+ // Check if a subject with the same value and type already exists in the database
+ const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData);
- if (subjectToRelate.$isNew) {
- await subjectToRelate.useTransaction(trx).save();
+ if (subject.$isNew === true) {
+ // If it's a completely new subject, create and associate it with the dataset
+ await dataset.useTransaction(trx).related('subjects').save(subject);
+ } else {
+ // If the subject already exists, just create the relationship
+ await dataset.useTransaction(trx).related('subjects').attach([subject.id]);
}
}
-
- // Ensure the relationship exists between dataset and subject
- const relationshipExists = await dataset.related('subjects').query().where('subject_id', subjectToRelate.id).first();
-
- if (!relationshipExists) {
- await dataset.useTransaction(trx).related('subjects').attach([subjectToRelate.id]);
- }
-
- // Track which subjects should remain associated with this dataset
- currentDatasetSubjectIds.add(subjectToRelate.id);
}
- // Handle explicit deletions
const subjectsToDelete = request.input('subjectsToDelete', []);
for (const subjectData of subjectsToDelete) {
if (subjectData.id) {
@@ -1300,16 +1211,16 @@ export default class DatasetController {
.withCount('datasets')
.firstOrFail();
- // Detach the subject from this dataset
- await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
+ // Check if the subject is used by multiple datasets
+ if (subject.$extras.datasets_count > 1) {
+ // If used by multiple datasets, just detach it from the current dataset
+ await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
+ } else {
+ // If only used by this dataset, delete the subject completely
- // If this was the only dataset using this subject, delete it entirely
- if (subject.$extras.datasets_count <= 1) {
+ await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
await subject.useTransaction(trx).delete();
}
-
- // Remove from current set if it was added earlier
- currentDatasetSubjectIds.delete(subjectData.id);
}
}
@@ -1488,26 +1399,16 @@ export default class DatasetController {
}
}
- public async delete({ request, inertia, response, session, auth }: HttpContext) {
+ public async delete({ request, inertia, response, session }: HttpContext) {
const id = request.param('id');
- const user = auth.user;
-
- // Check if user is authenticated
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
try {
- // This will throw 404 if dataset doesn't exist OR user doesn't own it
const dataset = await Dataset.query()
.preload('user', (builder) => {
builder.select('id', 'login');
})
.where('id', id)
- .where('account_id', user.id) // Only fetch if user owns it
.preload('files')
.firstOrFail();
-
const validStates = ['inprogress', 'rejected_editor'];
if (!validStates.includes(dataset.server_state)) {
// session.flash('errors', 'Invalid server state!');
@@ -1532,27 +1433,9 @@ export default class DatasetController {
}
}
- public async deleteUpdate({ params, session, response, auth }: HttpContext) {
+ public async deleteUpdate({ params, session, response }: HttpContext) {
try {
- const user = auth.user;
- if (!user) {
- return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
- }
-
- // This will throw 404 if dataset doesn't exist OR user doesn't own it
- const dataset = await Dataset.query()
- .where('id', params.id)
- .where('account_id', user.id) // Only fetch if user owns it
- .preload('files')
- .firstOrFail();
-
- // // Check if the authenticated user is the owner of the dataset
- // if (dataset.account_id !== user.id) {
- // return response
- // .flash(`Unauthorized access. You are not the owner of dataset with id ${params.id}.`, 'error')
- // .redirect()
- // .toRoute('dataset.list');
- // }
+ const dataset = await Dataset.query().where('id', params.id).preload('files').firstOrFail();
const validStates = ['inprogress', 'rejected_editor'];
if (validStates.includes(dataset.server_state)) {
diff --git a/app/Library/DatasetXmlSerializer.ts b/app/Library/DatasetXmlSerializer.ts
deleted file mode 100644
index f84d3b7..0000000
--- a/app/Library/DatasetXmlSerializer.ts
+++ /dev/null
@@ -1,231 +0,0 @@
-import DocumentXmlCache from '#models/DocumentXmlCache';
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
-import Dataset from '#models/dataset';
-import Strategy from './Strategy.js';
-import { builder } from 'xmlbuilder2';
-import logger from '@adonisjs/core/services/logger';
-
-/**
- * Configuration for XML serialization
- *
- * @interface XmlSerializationConfig
- */
-export interface XmlSerializationConfig {
- /** The dataset model to serialize */
- model: Dataset;
- /** DOM representation (if available) */
- dom?: XMLBuilder;
- /** Fields to exclude from serialization */
- excludeFields: Array;
- /** Whether to exclude empty fields */
- excludeEmpty: boolean;
- /** Base URI for xlink:ref elements */
- baseUri: string;
-}
-
-/**
- * Options for controlling serialization behavior
- */
-export interface SerializationOptions {
- /** Enable XML caching */
- enableCaching?: boolean;
- /** Exclude empty fields from output */
- excludeEmptyFields?: boolean;
- /** Custom base URI */
- baseUri?: string;
- /** Fields to exclude */
- excludeFields?: string[];
-}
-
-/**
- * DatasetXmlSerializer
- *
- * Handles XML serialization of Dataset models with intelligent caching.
- * Generates XML representations and manages cache lifecycle to optimize performance.
- *
- * @example
- * ```typescript
- * const serializer = new DatasetXmlSerializer(dataset);
- * serializer.enableCaching();
- * serializer.excludeEmptyFields();
- *
- * const xmlDocument = await serializer.toXmlDocument();
- * ```
- */
-export default class DatasetXmlSerializer {
- private readonly config: XmlSerializationConfig;
- private readonly strategy: Strategy;
- private cache: DocumentXmlCache | null = null;
- private cachingEnabled = false;
-
- constructor(dataset: Dataset, options: SerializationOptions = {}) {
- this.config = {
- model: dataset,
- excludeEmpty: options.excludeEmptyFields ?? false,
- baseUri: options.baseUri ?? '',
- excludeFields: options.excludeFields ?? [],
- };
-
- this.strategy = new Strategy({
- excludeEmpty: options.excludeEmptyFields ?? false,
- baseUri: options.baseUri ?? '',
- excludeFields: options.excludeFields ?? [],
- model: dataset,
- });
-
- if (options.enableCaching) {
- this.cachingEnabled = true;
- }
- }
-
- /**
- * Enable caching for XML generation
- * When enabled, generated XML is stored in database for faster retrieval
- */
- public enableCaching(): this {
- this.cachingEnabled = true;
- return this;
- }
-
- /**
- * Disable caching for XML generation
- */
- public disableCaching(): this {
- this.cachingEnabled = false;
- return this;
- }
-
- set model(model: Dataset) {
- this.config.model = model;
- }
-
- /**
- * Configure to exclude empty fields from XML output
- */
- public excludeEmptyFields(): this {
- this.config.excludeEmpty = true;
- return this;
- }
-
- /**
- * Set the cache instance directly (useful when preloading)
- * @param cache - The DocumentXmlCache instance
- */
- public setCache(cache: DocumentXmlCache): this {
- this.cache = cache;
- return this;
- }
-
- /**
- * Get the current cache instance
- */
- public getCache(): DocumentXmlCache | null {
- return this.cache;
- }
-
- /**
- * Get DOM document with intelligent caching
- * Returns cached version if valid, otherwise generates new document
- */
- public async toXmlDocument(): Promise {
- const dataset = this.config.model;
-
- // Try to get from cache first
- let cachedDocument: XMLBuilder | null = await this.retrieveFromCache();
-
- if (cachedDocument) {
- logger.debug(`Using cached XML for dataset ${dataset.id}`);
- return cachedDocument;
- }
-
- // Generate fresh document
- logger.debug(`[DatasetXmlSerializer] Cache miss - generating fresh XML for dataset ${dataset.id}`);
- const freshDocument = await this.strategy.createDomDocument();
-
- if (!freshDocument) {
- logger.error(`[DatasetXmlSerializer] Failed to generate XML for dataset ${dataset.id}`);
- return null;
- }
-
- // Cache if caching is enabled
- if (this.cachingEnabled) {
- await this.persistToCache(freshDocument, dataset);
- }
-
- // Extract the dataset-specific node
- return this.extractDatasetNode(freshDocument);
- }
-
- /**
- * Generate XML string representation
- * Convenience method that converts XMLBuilder to string
- */
- public async toXmlString(): Promise {
- const document = await this.toXmlDocument();
- return document ? document.end({ prettyPrint: false }) : null;
- }
-
- /**
- * Persist generated XML document to cache
- * Non-blocking - failures are logged but don't interrupt the flow
- */
- private async persistToCache(domDocument: XMLBuilder, dataset: Dataset): Promise {
- try {
- this.cache = this.cache || new DocumentXmlCache();
- this.cache.document_id = dataset.id;
- this.cache.xml_version = 1;
- this.cache.server_date_modified = dataset.server_date_modified.toFormat('yyyy-MM-dd HH:mm:ss');
- this.cache.xml_data = domDocument.end();
-
- await this.cache.save();
- logger.debug(`Cached XML for dataset ${dataset.id}`);
- } catch (error) {
- logger.error(`Failed to cache XML for dataset ${dataset.id}: ${error.message}`);
- // Don't throw - caching failure shouldn't break the flow
- }
- }
-
- /**
- * Extract the Rdr_Dataset node from full document
- */
- private extractDatasetNode(domDocument: XMLBuilder): XMLBuilder | null {
- const node = domDocument.find((n) => n.node.nodeName === 'Rdr_Dataset', false, true)?.node;
-
- if (node) {
- return builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node);
- }
-
- return domDocument;
- }
-
- /**
- * Attempt to retrieve valid cached XML document
- * Returns null if cache doesn't exist or is stale
- */
- private async retrieveFromCache(): Promise {
- const dataset: Dataset = this.config.model;
- if (!this.cache) {
- return null;
- }
-
- // Check if cache is still valid
- const actuallyCached = await DocumentXmlCache.hasValidEntry(dataset.id, dataset.server_date_modified);
-
- if (!actuallyCached) {
- logger.debug(`Cache invalid for dataset ${dataset.id}`);
- return null;
- }
-
- //cache is actual return cached document
- try {
- if (this.cache) {
- return this.cache.getDomDocument();
- } else {
- return null;
- }
- } catch (error) {
- logger.error(`Failed to retrieve cached document for dataset ${dataset.id}: ${error.message}`);
- return null;
- }
- }
-}
diff --git a/app/Library/Doi/DoiClient.ts b/app/Library/Doi/DoiClient.ts
index 4232ac4..86151e7 100644
--- a/app/Library/Doi/DoiClient.ts
+++ b/app/Library/Doi/DoiClient.ts
@@ -1,3 +1,6 @@
+// import { Client } from 'guzzle';
+// import { Log } from '@adonisjs/core/build/standalone';
+// import { DoiInterface } from './interfaces/DoiInterface';
import DoiClientContract from '#app/Library/Doi/DoiClientContract';
import DoiClientException from '#app/exceptions/DoiClientException';
import { StatusCodes } from 'http-status-codes';
@@ -9,14 +12,14 @@ export class DoiClient implements DoiClientContract {
public username: string;
public password: string;
public serviceUrl: string;
- public apiUrl: string;
constructor() {
// const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
this.username = process.env.DATACITE_USERNAME || '';
this.password = process.env.DATACITE_PASSWORD || '';
this.serviceUrl = process.env.DATACITE_SERVICE_URL || '';
- this.apiUrl = process.env.DATACITE_API_URL || 'https://api.datacite.org';
+ // this.prefix = process.env.DATACITE_PREFIX || '';
+ // this.base_domain = process.env.BASE_DOMAIN || '';
if (this.username === '' || this.password === '' || this.serviceUrl === '') {
const message = 'issing configuration settings to properly initialize DOI client';
@@ -87,240 +90,4 @@ export class DoiClient implements DoiClientContract {
throw new DoiClientException(error.response.status, error.response.data);
}
}
-
- /**
- * Retrieves DOI information from DataCite REST API
- *
- * @param doiValue The DOI identifier e.g. '10.5072/tethys.999'
- * @returns Promise with DOI information or null if not found
- */
- public async getDoiInfo(doiValue: string): Promise {
- try {
- // Use configurable DataCite REST API URL
- const dataciteApiUrl = `${this.apiUrl}/dois/${doiValue}`;
- const response = await axios.get(dataciteApiUrl, {
- headers: {
- Accept: 'application/vnd.api+json',
- },
- });
-
- if (response.status === 200 && response.data.data) {
- return {
- created: response.data.data.attributes.created,
- registered: response.data.data.attributes.registered,
- updated: response.data.data.attributes.updated,
- published: response.data.data.attributes.published,
- state: response.data.data.attributes.state,
- url: response.data.data.attributes.url,
- metadata: response.data.data.attributes,
- };
- }
- } catch (error) {
- if (error.response?.status === 404) {
- logger.debug(`DOI ${doiValue} not found in DataCite`);
- return null;
- }
-
- logger.debug(`DataCite REST API failed for ${doiValue}: ${error.message}`);
-
- // Fallback to MDS API
- return await this.getDoiInfoFromMds(doiValue);
- }
-
- return null;
- }
-
- /**
- * Fallback method to get DOI info from MDS API
- *
- * @param doiValue The DOI identifier
- * @returns Promise with basic DOI information or null
- */
- private async getDoiInfoFromMds(doiValue: string): Promise {
- try {
- const auth = {
- username: this.username,
- password: this.password,
- };
-
- // Get DOI URL
- const doiResponse = await axios.get(`${this.serviceUrl}/doi/${doiValue}`, { auth });
-
- if (doiResponse.status === 200) {
- // Get metadata if available
- try {
- const metadataResponse = await axios.get(`${this.serviceUrl}/metadata/${doiValue}`, {
- auth,
- headers: {
- Accept: 'application/xml',
- },
- });
-
- return {
- url: doiResponse.data.trim(),
- metadata: metadataResponse.data,
- created: new Date().toISOString(), // MDS doesn't provide creation dates
- registered: new Date().toISOString(), // Use current time as fallback
- source: 'mds',
- };
- } catch (metadataError) {
- // Return basic info even if metadata fetch fails
- return {
- url: doiResponse.data.trim(),
- created: new Date().toISOString(),
- registered: new Date().toISOString(),
- source: 'mds',
- };
- }
- }
- } catch (error) {
- if (error.response?.status === 404) {
- logger.debug(`DOI ${doiValue} not found in DataCite MDS`);
- return null;
- }
-
- logger.debug(`DataCite MDS API failed for ${doiValue}: ${error.message}`);
- }
-
- return null;
- }
-
- /**
- * Checks if a DOI exists in DataCite
- *
- * @param doiValue The DOI identifier
- * @returns Promise True if DOI exists
- */
- public async doiExists(doiValue: string): Promise {
- const doiInfo = await this.getDoiInfo(doiValue);
- return doiInfo !== null;
- }
-
- /**
- * Gets the last modification date of a DOI
- *
- * @param doiValue The DOI identifier
- * @returns Promise Last modification date or creation date if never updated, null if not found
- */
- public async getDoiLastModified(doiValue: string): Promise {
- const doiInfo = await this.getDoiInfo(doiValue);
-
- if (doiInfo) {
- // Use updated date if available, otherwise fall back to created/registered date
- const dateToUse = doiInfo.updated || doiInfo.registered || doiInfo.created;
-
- if (dateToUse) {
- logger.debug(
- `DOI ${doiValue}: Using ${doiInfo.updated ? 'updated' : doiInfo.registered ? 'registered' : 'created'} date: ${dateToUse}`,
- );
- return new Date(dateToUse);
- }
- }
-
- return null;
- }
-
- /**
- * Makes a DOI unfindable (registered but not discoverable)
- * Note: DOIs cannot be deleted, only made unfindable
- * await doiClient.makeDoiUnfindable('10.21388/tethys.231');
- *
- * @param doiValue The DOI identifier e.g. '10.5072/tethys.999'
- * @returns Promise> The http response
- */
- public async makeDoiUnfindable(doiValue: string): Promise> {
- const auth = {
- username: this.username,
- password: this.password,
- };
-
- try {
- // First, check if DOI exists
- const exists = await this.doiExists(doiValue);
- if (!exists) {
- throw new DoiClientException(404, `DOI ${doiValue} not found`);
- }
-
- // Delete the DOI URL mapping to make it unfindable
- // This removes the URL but keeps the metadata registered
- const response = await axios.delete(`${this.serviceUrl}/doi/${doiValue}`, { auth });
-
- // Response Codes for DELETE /doi/{doi}
- // 200 OK: operation successful
- // 401 Unauthorized: no login
- // 403 Forbidden: login problem, quota exceeded
- // 404 Not Found: DOI does not exist
- if (response.status !== 200) {
- const message = `Unexpected DataCite MDS response code ${response.status}`;
- logger.error(message);
- throw new DoiClientException(response.status, message);
- }
-
- logger.info(`DOI ${doiValue} successfully made unfindable`);
- return response;
- } catch (error) {
- logger.error(`Failed to make DOI ${doiValue} unfindable: ${error.message}`);
- if (error instanceof DoiClientException) {
- throw error;
- }
- throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message);
- }
- }
-
- /**
- * Makes a DOI findable again by re-registering the URL
- * await doiClient.makeDoiFindable(
- * '10.21388/tethys.231',
- * 'https://doi.dev.tethys.at/10.21388/tethys.231'
- * );
- *
- * @param doiValue The DOI identifier e.g. '10.5072/tethys.999'
- * @param landingPageUrl The landing page URL
- * @returns Promise> The http response
- */
- public async makeDoiFindable(doiValue: string, landingPageUrl: string): Promise> {
- const auth = {
- username: this.username,
- password: this.password,
- };
-
- try {
- // Re-register the DOI with its URL to make it findable again
- const response = await axios.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, { auth });
-
- // Response Codes for PUT /doi/{doi}
- // 201 Created: operation successful
- // 400 Bad Request: request body must be exactly two lines: DOI and URL
- // 401 Unauthorized: no login
- // 403 Forbidden: login problem, quota exceeded
- // 412 Precondition failed: metadata must be uploaded first
- if (response.status !== 201) {
- const message = `Unexpected DataCite MDS response code ${response.status}`;
- logger.error(message);
- throw new DoiClientException(response.status, message);
- }
-
- logger.info(`DOI ${doiValue} successfully made findable again`);
- return response;
- } catch (error) {
- logger.error(`Failed to make DOI ${doiValue} findable: ${error.message}`);
- if (error instanceof DoiClientException) {
- throw error;
- }
- throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message);
- }
- }
-
- /**
- * Gets the current state of a DOI (draft, registered, findable)
- * const state = await doiClient.getDoiState('10.21388/tethys.231');
- * console.log(`Current state: ${state}`); // 'findable'
- *
- * @param doiValue The DOI identifier
- * @returns Promise The DOI state or null if not found
- */
- public async getDoiState(doiValue: string): Promise {
- const doiInfo = await this.getDoiInfo(doiValue);
- return doiInfo?.state || null;
- }
}
diff --git a/app/Library/Utils/Index.ts b/app/Library/Utils/Index.ts
index 20253a4..9bc21f7 100644
--- a/app/Library/Utils/Index.ts
+++ b/app/Library/Utils/Index.ts
@@ -2,7 +2,7 @@ import Dataset from '#models/dataset';
import { Client } from '@opensearch-project/opensearch';
import { create } from 'xmlbuilder2';
import SaxonJS from 'saxon-js';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import logger from '@adonisjs/core/services/logger';
import { readFileSync } from 'fs';
@@ -72,42 +72,31 @@ export default {
}
},
- /**
- * Index a dataset document to OpenSearch/Elasticsearch
- */
async indexDocument(dataset: Dataset, index_name: string): Promise {
try {
- // Load XSLT transformation file
- const xsltProc = readFileSync('public/assets2/solr.sef.json');
+ const proc = readFileSync('public/assets2/solr.sef.json');
+ const doc: string = await this.getTransformedString(dataset, proc);
- // Transform dataset to JSON document
- const jsonDoc: string = await this.getTransformedString(dataset, xsltProc);
-
- const document = JSON.parse(jsonDoc);
-
- // Index document to OpenSearch with doument json body
+ let document = JSON.parse(doc);
await this.client.index({
id: dataset.publish_id?.toString(),
index: index_name,
body: document,
- refresh: true, // make immediately searchable
+ refresh: true,
});
- logger.info(`Dataset ${dataset.publish_id} successfully indexed to ${index_name}`);
+ logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
} catch (error) {
- logger.error(`Failed to index dataset ${dataset.publish_id}: ${error.message}`);
- throw error; // Re-throw to allow caller to handle
+ logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
}
},
- /**
- * Transform dataset XML to JSON using XSLT
- */
async getTransformedString(dataset: Dataset, proc: Buffer): Promise {
- // Generate XML string from dataset
- const xmlString = await this.generateDatasetXml(dataset);
+ let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '');
+ const datasetNode = xml.root().ele('Dataset');
+ await createXmlRecord(dataset, datasetNode);
+ const xmlString = xml.end({ prettyPrint: false });
try {
- // Apply XSLT transformation
const result = await SaxonJS.transform({
stylesheetText: proc,
destination: 'serialized',
@@ -119,18 +108,6 @@ export default {
return '';
}
},
-
- /**
- * Generate XML string from dataset model
- */
- async generateDatasetXml(dataset: Dataset): Promise {
- const xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '');
- const datasetNode = xml.root().ele('Dataset');
-
- await createXmlRecord(dataset, datasetNode);
-
- return xml.end({ prettyPrint: false });
- },
};
/**
* Return the default global focus trap stack
@@ -138,49 +115,74 @@ export default {
* @return {import('focus-trap').FocusTrap[]}
*/
-/**
- * Create complete XML record for dataset
- * Handles caching and metadata enrichment
- */
+// export const indexDocument = async (dataset: Dataset, index_name: string, proc: Buffer): Promise => {
+// try {
+// const doc = await getJsonString(dataset, proc);
+
+// let document = JSON.parse(doc);
+// await client.index({
+// id: dataset.publish_id?.toString(),
+// index: index_name,
+// body: document,
+// refresh: true,
+// });
+// Logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
+// } catch (error) {
+// Logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
+// }
+// };
+
+// const getJsonString = async (dataset, proc): Promise => {
+// let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '');
+// const datasetNode = xml.root().ele('Dataset');
+// await createXmlRecord(dataset, datasetNode);
+// const xmlString = xml.end({ prettyPrint: false });
+
+// try {
+// const result = await transform({
+// stylesheetText: proc,
+// destination: 'serialized',
+// sourceText: xmlString,
+// });
+// return result.principalResult;
+// } catch (error) {
+// Logger.error(`An error occurred while creating the user, error: ${error.message},`);
+// return '';
+// }
+// };
+
const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise => {
const domNode = await getDatasetXmlDomNode(dataset);
-
- if (!domNode) {
- throw new Error(`Failed to generate XML DOM node for dataset ${dataset.id}`);
- }
-
- // Enrich with landing page URL
- if (dataset.publish_id) {
- addLandingPageAttribute(domNode, dataset.publish_id.toString());
- }
-
- // Add data type specification
- addSpecInformation(domNode, `data-type:${dataset.type}`);
-
- // Add collection information
- if (dataset.collections) {
- for (const coll of dataset.collections) {
- const collRole = coll.collectionRole;
- addSpecInformation(domNode, `${collRole.oai_name}:${coll.number}`);
+ if (domNode) {
+ // add frontdoor url and data-type
+ dataset.publish_id && addLandingPageAttribute(domNode, dataset.publish_id.toString());
+ addSpecInformation(domNode, 'data-type:' + dataset.type);
+ if (dataset.collections) {
+ for (const coll of dataset.collections) {
+ const collRole = coll.collectionRole;
+ addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
+ }
}
- }
- datasetNode.import(domNode);
+ datasetNode.import(domNode);
+ }
};
const getDatasetXmlDomNode = async (dataset: Dataset): Promise => {
- const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
+ const xmlModel = new XmlModel(dataset);
// xmlModel.setModel(dataset);
-
- // Load cache relationship if not already loaded
+ xmlModel.excludeEmptyFields();
+ xmlModel.caching = true;
+ // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+ // dataset.load('xmlCache');
await dataset.load('xmlCache');
if (dataset.xmlCache) {
- serializer.setCache(dataset.xmlCache);
+ xmlModel.xmlCache = dataset.xmlCache;
}
- // Generate or retrieve cached DOM document
- const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
- return xmlDocument;
+ // return cache.getDomDocument();
+ const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+ return domDocument;
};
const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
@@ -190,6 +192,6 @@ const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
domNode.att('landingpage', url);
};
-const addSpecInformation = (domNode: XMLBuilder, information: string) => {
+const addSpecInformation= (domNode: XMLBuilder, information: string) => {
domNode.ele('SetSpec').att('Value', information);
-};
+};
\ No newline at end of file
diff --git a/app/Library/XmlModel.ts b/app/Library/XmlModel.ts
new file mode 100644
index 0000000..6f76474
--- /dev/null
+++ b/app/Library/XmlModel.ts
@@ -0,0 +1,129 @@
+import DocumentXmlCache from '#models/DocumentXmlCache';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
+import Dataset from '#models/dataset';
+import Strategy from './Strategy.js';
+import { DateTime } from 'luxon';
+import { builder } from 'xmlbuilder2';
+
+/**
+ * This is the description of the interface
+ *
+ * @interface Conf
+ * @member {Model} model holds the current dataset model
+ * @member {XMLBuilder} dom holds the current DOM representation
+ * @member {Array} excludeFields List of fields to skip on serialization.
+ * @member {boolean} excludeEmpty True, if empty fields get excluded from serialization.
+ * @member {string} baseUri Base URI for xlink:ref elements
+ */
+export interface Conf {
+ model: Dataset;
+ dom?: XMLBuilder;
+ excludeFields: Array;
+ excludeEmpty: boolean;
+ baseUri: string;
+}
+
+export default class XmlModel {
+ private config: Conf;
+ // private strategy = null;
+ private cache: DocumentXmlCache | null = null;
+ private _caching = false;
+ private strategy: Strategy;
+
+ constructor(dataset: Dataset) {
+ // $this->strategy = new Strategy();// Opus_Model_Xml_Version1;
+ // $this->config = new Conf();
+ // $this->strategy->setup($this->config);
+
+ this.config = {
+ excludeEmpty: false,
+ baseUri: '',
+ excludeFields: [],
+ model: dataset,
+ };
+
+ this.strategy = new Strategy({
+ excludeEmpty: true,
+ baseUri: '',
+ excludeFields: [],
+ model: dataset,
+ });
+ }
+
+ set model(model: Dataset) {
+ this.config.model = model;
+ }
+
+ public excludeEmptyFields(): void {
+ this.config.excludeEmpty = true;
+ }
+
+ get xmlCache(): DocumentXmlCache | null {
+ return this.cache;
+ }
+
+ set xmlCache(cache: DocumentXmlCache) {
+ this.cache = cache;
+ }
+
+ get caching(): boolean {
+ return this._caching;
+ }
+ set caching(caching: boolean) {
+ this._caching = caching;
+ }
+
+ public async getDomDocument(): Promise {
+ const dataset = this.config.model;
+
+ let domDocument: XMLBuilder | null = await this.getDomDocumentFromXmlCache();
+ if (domDocument == null) {
+ domDocument = await this.strategy.createDomDocument();
+ // domDocument = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '');
+ if (this._caching) {
+ // caching is desired:
+ this.cache = this.cache || new DocumentXmlCache();
+ this.cache.document_id = dataset.id;
+ this.cache.xml_version = 1; // (int)$this->strategy->getVersion();
+ this.cache.server_date_modified = dataset.server_date_modified.toFormat('yyyy-MM-dd HH:mm:ss');
+ this.cache.xml_data = domDocument.end();
+ await this.cache.save();
+ }
+ const node = domDocument.find(
+ (n) => {
+ const test = n.node.nodeName == 'Rdr_Dataset';
+ return test;
+ },
+ false,
+ true,
+ )?.node;
+ if (node != undefined) {
+ domDocument = builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node);
+ }
+ }
+ return domDocument;
+ }
+
+ private async getDomDocumentFromXmlCache(): Promise {
+ const dataset: Dataset = this.config.model;
+ if (!this.cache) {
+ return null;
+ }
+ //.toFormat('YYYY-MM-DD HH:mm:ss');
+ let date: DateTime = dataset.server_date_modified;
+ const actuallyCached: boolean = await DocumentXmlCache.hasValidEntry(dataset.id, date);
+ if (!actuallyCached) {
+ return null;
+ }
+ //cache is actual return it for oai:
+ try {
+ if (this.cache) {
+ return this.cache.getDomDocument();
+ } else {
+ return null;
+ }
+ } catch (error) {
+ return null;
+ }
+ }
+}
diff --git a/app/controllers/projects_controller.ts b/app/controllers/projects_controller.ts
deleted file mode 100644
index 21e20df..0000000
--- a/app/controllers/projects_controller.ts
+++ /dev/null
@@ -1,54 +0,0 @@
-// app/controllers/projects_controller.ts
-import Project from '#models/project';
-import type { HttpContext } from '@adonisjs/core/http';
-import { createProjectValidator, updateProjectValidator } from '#validators/project';
-
-export default class ProjectsController {
- // GET /settings/projects
- public async index({ inertia, auth }: HttpContext) {
- const projects = await Project.all();
- // return inertia.render('Admin/Project/Index', { projects });
- return inertia.render('Admin/Project/Index', {
- projects: projects,
- can: {
- edit: await auth.user?.can(['settings']),
- create: await auth.user?.can(['settings']),
- },
- });
- }
-
- // GET /settings/projects/create
- public async create({ inertia }: HttpContext) {
- return inertia.render('Admin/Project/Create');
- }
-
- // POST /settings/projects
- public async store({ request, response, session }: HttpContext) {
- // Validate the request data
- const data = await request.validateUsing(createProjectValidator);
-
- await Project.create(data);
-
- session.flash('success', 'Project created successfully');
- return response.redirect().toRoute('settings.project.index');
- }
-
- // GET /settings/projects/:id/edit
- public async edit({ params, inertia }: HttpContext) {
- const project = await Project.findOrFail(params.id);
- return inertia.render('Admin/Project/Edit', { project });
- }
-
- // PUT /settings/projects/:id
- public async update({ params, request, response, session }: HttpContext) {
- const project = await Project.findOrFail(params.id);
-
- // Validate the request data
- const data = await request.validateUsing(updateProjectValidator);
-
- await project.merge(data).save();
-
- session.flash('success', 'Project updated successfully');
- return response.redirect().toRoute('settings.project.index');
- }
-}
diff --git a/app/models/DocumentXmlCache.ts b/app/models/DocumentXmlCache.ts
index de8defc..ed7315e 100644
--- a/app/models/DocumentXmlCache.ts
+++ b/app/models/DocumentXmlCache.ts
@@ -4,8 +4,7 @@ import { builder, create } from 'xmlbuilder2';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import db from '@adonisjs/lucid/services/db';
import { DateTime } from 'luxon';
-import type { BelongsTo } from '@adonisjs/lucid/types/relations';
-import logger from '@adonisjs/core/services/logger';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
export default class DocumentXmlCache extends BaseModel {
public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -67,38 +66,33 @@ export default class DocumentXmlCache extends BaseModel {
}
/**
- * Check if a valid (non-stale) cache entry exists
- * Cache is valid only if it was created AFTER the dataset's last modification
+ * Check if a dataset in a specific xml version is already cached or not.
*
- * @param datasetId - The dataset ID to check
- * @param datasetServerDateModified - The dataset's last modification timestamp
- * @returns true if valid cache exists, false otherwise
+ * @param mixed datasetId
+ * @param mixed serverDateModified
+ * @returns {Promise} Returns true on cached hit else false.
*/
+ // public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise {
+ // // const formattedDate = dayjs(datasetServerDateModified).format('YYYY-MM-DD HH:mm:ss');
+
+ // const query = Database.from(this.table)
+ // .where('document_id', datasetId)
+ // .where('server_date_modified', '2023-08-17 16:51:03')
+ // .first();
+
+ // const row = await query;
+ // return !!row;
+ // }
+
+ // Assuming 'DocumentXmlCache' has a table with a 'server_date_modified' column in your database
public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise {
const serverDateModifiedString: string = datasetServerDateModified.toFormat('yyyy-MM-dd HH:mm:ss'); // Convert DateTime to ISO string
-
- const row = await db
- .from(this.table)
+ const query = db.from(this.table)
.where('document_id', datasetId)
- .where('server_date_modified', '>', serverDateModifiedString) // Check if server_date_modified is newer or equal
+ .where('server_date_modified', '>=', serverDateModifiedString) // Check if server_date_modified is newer or equal
.first();
- const isValid = !!row;
-
- if (isValid) {
- logger.debug(`Valid cache found for dataset ${datasetId}`);
- } else {
- logger.debug(`No valid cache for dataset ${datasetId} (dataset modified: ${serverDateModifiedString})`);
- }
-
- return isValid;
- }
-
- /**
- * Invalidate (delete) cache entry
- */
- public async invalidate(): Promise {
- await this.delete();
- logger.debug(`Invalidated cache for document ${this.document_id}`);
+ const row = await query;
+ return !!row;
}
}
diff --git a/app/models/person.ts b/app/models/person.ts
index f4cf3a2..cdc612d 100644
--- a/app/models/person.ts
+++ b/app/models/person.ts
@@ -30,7 +30,7 @@ export default class Person extends BaseModel {
@column({})
public lastName: string;
- @column({ columnName: 'identifier_orcid' })
+ @column({})
public identifierOrcid: string;
@column({})
@@ -95,34 +95,4 @@ export default class Person extends BaseModel {
pivotColumns: ['role', 'sort_order', 'allow_email_contact'],
})
public datasets: ManyToMany;
-
- // public toJSON() {
- // const json = super.toJSON();
-
- // // Check if this person is loaded through a pivot relationship with sensitive roles
- // const pivotRole = this.$extras?.pivot_role;
- // if (pivotRole === 'author' || pivotRole === 'contributor') {
- // // Remove sensitive information for public-facing roles
- // delete json.email;
- // // delete json.identifierOrcid;
- // }
-
- // return json;
- // }
-
- // @afterFind()
- // public static async afterFindHook(person: Person) {
- // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') {
- // person.email = undefined as any;
- // }
- // }
-
- // @afterFetch()
- // public static async afterFetchHook(persons: Person[]) {
- // persons.forEach(person => {
- // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') {
- // person.email = undefined as any;
- // }
- // });
- // }
}
diff --git a/app/models/user.ts b/app/models/user.ts
index 7be02b9..5dbaab4 100644
--- a/app/models/user.ts
+++ b/app/models/user.ts
@@ -89,11 +89,24 @@ export default class User extends compose(BaseModel, AuthFinder) {
@column({})
public avatar: string;
+ // @hasOne(() => TotpSecret, {
+ // foreignKey: 'user_id',
+ // })
+ // public totp_secret: HasOne;
+
+ // @beforeSave()
+ // public static async hashPassword(user: User) {
+ // if (user.$dirty.password) {
+ // user.password = await hash.use('laravel').make(user.password);
+ // }
+ // }
+
public get isTwoFactorEnabled(): boolean {
return Boolean(this?.twoFactorSecret && this.state == TotpState.STATE_ENABLED);
// return Boolean(this.totp_secret?.twoFactorSecret);
}
+
@manyToMany(() => Role, {
pivotForeignKey: 'account_id',
pivotRelatedForeignKey: 'role_id',
@@ -129,9 +142,7 @@ export default class User extends compose(BaseModel, AuthFinder) {
@beforeFind()
@beforeFetch()
public static preloadRoles(user: User) {
- user.preload('roles', (builder) => {
- builder.select(['id', 'name', 'display_name', 'description']);
- });
+ user.preload('roles')
}
public async getBackupCodes(this: User): Promise {
diff --git a/app/validators/dataset.ts b/app/validators/dataset.ts
index f670b81..5417463 100644
--- a/app/validators/dataset.ts
+++ b/app/validators/dataset.ts
@@ -55,8 +55,8 @@ export const createDatasetValidator = vine.compile(
.translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
}),
)
- // .minLength(1),
- .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
+ // .minLength(1),
+ .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
authors: vine
.array(
vine.object({
@@ -67,9 +67,8 @@ export const createDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.minLength(1)
@@ -84,10 +83,9 @@ export const createDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.distinct('email')
@@ -160,8 +158,7 @@ export const createDatasetValidator = vine.compile(
.fileScan({ removeInfected: true }),
)
.minLength(1),
- }),
-);
+ }),);
/**
* Validates the dataset's update action
@@ -217,9 +214,8 @@ export const updateDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.minLength(1)
@@ -234,9 +230,8 @@ export const updateDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
}),
)
@@ -310,13 +305,12 @@ export const updateDatasetValidator = vine.compile(
.fileScan({ removeInfected: true }),
)
.dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }),
- fileInputs: vine
- .array(
- vine.object({
- label: vine.string().trim().maxLength(100),
- }),
- )
- .optional(),
+ fileInputs: vine.array(
+ vine.object({
+ label: vine.string().trim().maxLength(100),
+ //extnames: extensions,
+ }),
+ ),
}),
);
@@ -371,9 +365,8 @@ export const updateEditorDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
}),
)
.minLength(1)
@@ -388,9 +381,8 @@ export const updateEditorDatasetValidator = vine.compile(
.email()
.normalizeEmail()
.isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
- first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+ first_name: vine.string().trim().minLength(3).maxLength(255),
last_name: vine.string().trim().minLength(3).maxLength(255),
- identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
}),
)
@@ -504,7 +496,7 @@ let messagesProvider = new SimpleMessagesProvider({
'files.array.minLength': 'At least {{ min }} file upload is required.',
'files.*.size': 'file size is to big',
'files.*.extnames': 'file extension is not supported',
- 'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`,
+ 'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`,
});
createDatasetValidator.messagesProvider = messagesProvider;
diff --git a/app/validators/project.ts b/app/validators/project.ts
deleted file mode 100644
index 7f3d1f8..0000000
--- a/app/validators/project.ts
+++ /dev/null
@@ -1,28 +0,0 @@
-// app/validators/project.ts
-import vine from '@vinejs/vine';
-
-export const createProjectValidator = vine.compile(
- vine.object({
- label: vine.string().trim().minLength(1).maxLength(50) .regex(/^[a-z0-9-]+$/),
- name: vine
- .string()
- .trim()
- .minLength(3)
- .maxLength(255)
- .regex(/^[a-zA-Z0-9รครถรผรรรร\s-]+$/),
- description: vine.string().trim().maxLength(255).minLength(5).optional(),
- }),
-);
-
-export const updateProjectValidator = vine.compile(
- vine.object({
- // label is NOT included since it's readonly
- name: vine
- .string()
- .trim()
- .minLength(3)
- .maxLength(255)
- .regex(/^[a-zA-Z0-9รครถรผรรรร\s-]+$/),
- description: vine.string().trim().maxLength(255).minLength(5).optional(),
- }),
-);
diff --git a/app/validators/role.ts b/app/validators/role.ts
index 81262d9..61e8ecd 100644
--- a/app/validators/role.ts
+++ b/app/validators/role.ts
@@ -8,20 +8,20 @@ export const createRoleValidator = vine.compile(
vine.object({
name: vine
.string()
+ .isUnique({ table: 'roles', column: 'name' })
.trim()
.minLength(3)
.maxLength(255)
- .isUnique({ table: 'roles', column: 'name' })
- .regex(/^[a-zA-Z0-9]+$/), // Must be alphanumeric
+ .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
display_name: vine
.string()
+ .isUnique({ table: 'roles', column: 'display_name' })
.trim()
.minLength(3)
.maxLength(255)
- .isUnique({ table: 'roles', column: 'display_name' })
.regex(/^[a-zA-Z0-9]+$/),
description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
- permissions: vine.array(vine.number()).minLength(1), // At least one permission required
+ permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
}),
);
@@ -29,28 +29,21 @@ export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compi
vine.object({
name: vine
.string()
- .trim()
- .minLength(3)
- .maxLength(255)
+ // .unique(async (db, value, field) => {
+ // const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first();
+ // return result.length ? false : true;
+ // })
.isUnique({
table: 'roles',
column: 'name',
whereNot: (field) => field.meta.roleId,
})
- .regex(/^[a-zA-Z0-9]+$/),
- display_name: vine
- .string()
.trim()
.minLength(3)
- .maxLength(255)
- .isUnique({
- table: 'roles',
- column: 'display_name',
- whereNot: (field) => field.meta.roleId,
- })
- .regex(/^[a-zA-Z0-9]+$/),
+ .maxLength(255),
+
description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
- permissions: vine.array(vine.number()).minLength(1), // At least one permission required
+ permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
}),
);
diff --git a/clamd.conf b/clamd.conf
index f066387..171396d 100644
--- a/clamd.conf
+++ b/clamd.conf
@@ -5,23 +5,7 @@ LogSyslog no
LogVerbose yes
DatabaseDirectory /var/lib/clamav
LocalSocket /var/run/clamav/clamd.socket
-# LocalSocketMode 666
-# Optional: allow multiple threads
-MaxThreads 20
-# Disable TCP socket
-# TCPSocket 0
-
-# TCP port address.
-# Default: no
-# TCPSocket 3310
-# TCP address.
-# By default we bind to INADDR_ANY, probably not wise.
-# Enable the following to provide some degree of protection
-# from the outside world.
-# Default: no
-# TCPAddr 127.0.0.1
-
Foreground no
PidFile /var/run/clamav/clamd.pid
-# LocalSocketGroup node # Changed from 'clamav'
-# User node # Changed from 'clamav' - clamd runs as clamav user
\ No newline at end of file
+LocalSocketGroup node
+User node
\ No newline at end of file
diff --git a/commands/fix_dataset_cross_references.ts b/commands/fix_dataset_cross_references.ts
deleted file mode 100644
index baa2e0e..0000000
--- a/commands/fix_dataset_cross_references.ts
+++ /dev/null
@@ -1,482 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command fix-dataset-cross-references
-| DONE: create commands/fix_dataset_cross_references.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import type { CommandOptions } from '@adonisjs/core/types/ace';
-import { DateTime } from 'luxon';
-import Dataset from '#models/dataset';
-import DatasetReference from '#models/dataset_reference';
-import AppConfig from '#models/appconfig';
-// import env from '#start/env';
-
-interface MissingCrossReference {
- sourceDatasetId: number;
- targetDatasetId: number;
- sourcePublishId: number | null;
- targetPublishId: number | null;
- sourceDoi: string | null;
- targetDoi: string | null;
- referenceType: string;
- relation: string;
- doi: string | null;
- reverseRelation: string;
- sourceReferenceLabel: string | null;
-}
-
-export default class DetectMissingCrossReferences extends BaseCommand {
- static commandName = 'detect:missing-cross-references';
- static description = 'Detect missing bidirectional cross-references between versioned datasets';
-
- public static needsApplication = true;
-
- @flags.boolean({ alias: 'f', description: 'Fix missing cross-references automatically' })
- public fix: boolean = false;
-
- @flags.boolean({ alias: 'v', description: 'Verbose output' })
- public verbose: boolean = false;
-
- @flags.number({ alias: 'p', description: 'Filter by specific publish_id (source or target dataset)' })
- public publish_id?: number;
-
- // example: node ace detect:missing-cross-references --verbose -p 227 //if you want to filter by specific publish_id with details
- // example: node ace detect:missing-cross-references --verbose
- // example: node ace detect:missing-cross-references --fix -p 227 //if you want to filter by specific publish_id and fix it
- // example: node ace detect:missing-cross-references
-
- public static options: CommandOptions = {
- startApp: true,
- staysAlive: false,
- };
-
- // Define the allowed relations that we want to process
- private readonly ALLOWED_RELATIONS = [
- 'IsNewVersionOf',
- 'IsPreviousVersionOf',
- 'IsVariantFormOf',
- 'IsOriginalFormOf',
- 'Continues',
- 'IsContinuedBy',
- 'HasPart',
- 'IsPartOf',
- ];
- // private readonly ALLOWED_RELATIONS = ['IsPreviousVersionOf', 'IsOriginalFormOf'];
-
- async run() {
- this.logger.info('๐ Detecting missing cross-references...');
- this.logger.info(`๐ Processing only these relations: ${this.ALLOWED_RELATIONS.join(', ')}`);
-
- if (this.publish_id) {
- this.logger.info(`Filtering by publish_id: ${this.publish_id}`);
- }
-
- try {
- const missingReferences = await this.findMissingCrossReferences();
-
- // Store count in AppConfig if not fixing and count >= 1
- if (!this.fix && missingReferences.length >= 1) {
- await this.storeMissingCrossReferencesCount(missingReferences.length);
- }
-
- if (missingReferences.length === 0) {
- const filterMsg = this.publish_id ? ` for publish_id ${this.publish_id}` : '';
- this.logger.success(`All cross-references are properly linked for the specified relations${filterMsg}!`);
- // Clear the count if no missing references
- if (!this.fix) {
- await this.storeMissingCrossReferencesCount(0);
- }
- return;
- }
-
- const filterMsg = this.publish_id ? ` (filtered by publish_id ${this.publish_id})` : '';
- this.logger.warning(`Found ${missingReferences.length} missing cross-reference(s)${filterMsg}:`);
-
- // Show brief list if not verbose mode
- if (!this.verbose) {
- for (const missing of missingReferences) {
- const sourceDoi = missing.sourceDoi ? ` DOI: ${missing.sourceDoi}` : '';
- const targetDoi = missing.targetDoi ? ` DOI: ${missing.targetDoi}` : '';
-
- this.logger.info(
- `Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId}${sourceDoi}) ${missing.relation} Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId}${targetDoi}) โ missing reverse: ${missing.reverseRelation}`,
- );
- }
- } else {
- // Verbose mode - show detailed info
- for (const missing of missingReferences) {
- this.logger.info(
- `Dataset ${missing.sourceDatasetId} references ${missing.targetDatasetId}, but reverse reference is missing`,
- );
- this.logger.info(` - Reference type: ${missing.referenceType}`);
- this.logger.info(` - Relation: ${missing.relation}`);
- this.logger.info(` - DOI: ${missing.doi}`);
- }
- }
-
- if (this.fix) {
- await this.fixMissingReferences(missingReferences);
- // Clear the count after fixing
- await this.storeMissingCrossReferencesCount(0);
- this.logger.success('All missing cross-references have been fixed!');
- } else {
- if (this.verbose) {
- this.printMissingReferencesList(missingReferences);
- }
- this.logger.info('๐ก Run with --fix flag to automatically create missing cross-references');
- if (this.publish_id) {
- this.logger.info(`๐ฏ Currently filtering by publish_id: ${this.publish_id}`);
- }
- }
- } catch (error) {
- this.logger.error('Error detecting missing cross-references:', error);
- process.exit(1);
- }
- }
-
- private async storeMissingCrossReferencesCount(count: number): Promise {
- try {
- await AppConfig.updateOrCreate(
- {
- appid: 'commands',
- configkey: 'missing_cross_references_count',
- },
- {
- configvalue: count.toString(),
- },
- );
-
- this.logger.info(`๐ Stored missing cross-references count in database: ${count}`);
- } catch (error) {
- this.logger.error('Failed to store missing cross-references count:', error);
- }
- }
-
- private async findMissingCrossReferences(): Promise {
- const missingReferences: {
- sourceDatasetId: number;
- targetDatasetId: number;
- sourcePublishId: number | null;
- targetPublishId: number | null;
- sourceDoi: string | null;
- targetDoi: string | null;
- referenceType: string;
- relation: string;
- doi: string | null;
- reverseRelation: string;
- sourceReferenceLabel: string | null;
- }[] = [];
-
- this.logger.info('๐ Querying dataset references...');
-
- // Find all references that point to Tethys datasets (DOI or URL containing tethys DOI)
- // Only from datasets that are published AND only for allowed relations
- const tethysReferencesQuery = DatasetReference.query()
- .whereIn('type', ['DOI', 'URL'])
- .whereIn('relation', this.ALLOWED_RELATIONS) // Only process allowed relations
- .where((query) => {
- query.where('value', 'like', '%doi.org/10.24341/tethys.%').orWhere('value', 'like', '%tethys.at/dataset/%');
- })
- .preload('dataset', (datasetQuery) => {
- datasetQuery.preload('identifier');
- })
- .whereHas('dataset', (datasetQuery) => {
- datasetQuery.where('server_state', 'published');
- });
- if (typeof this.publish_id === 'number') {
- tethysReferencesQuery.whereHas('dataset', (datasetQuery) => {
- datasetQuery.where('publish_id', this.publish_id as number);
- });
- }
-
- const tethysReferences = await tethysReferencesQuery.exec();
-
- this.logger.info(`๐ Found ${tethysReferences.length} Tethys references from published datasets (allowed relations only)`);
-
- let processedCount = 0;
- let skippedCount = 0;
-
- for (const reference of tethysReferences) {
- processedCount++;
-
- // if (this.verbose && processedCount % 10 === 0) {
- // this.logger.info(`๐ Processed ${processedCount}/${tethysReferences.length} references...`);
- // }
-
- // Double-check that this relation is in our allowed list (safety check)
- if (!this.ALLOWED_RELATIONS.includes(reference.relation)) {
- skippedCount++;
- if (this.verbose) {
- this.logger.info(`โญ๏ธ Skipping relation "${reference.relation}" - not in allowed list`);
- }
- continue;
- }
-
- // Extract dataset publish_id from DOI or URL
- // const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value);
- // Extract DOI from reference URL
- const doi = this.extractDoiFromReference(reference.value);
-
- // if (!targetDatasetPublish) {
- // if (this.verbose) {
- // this.logger.warning(`Could not extract publish ID from: ${reference.value}`);
- // }
- // continue;
- // }
- if (!doi) {
- if (this.verbose) {
- this.logger.warning(`Could not extract DOI from: ${reference.value}`);
- }
- continue;
- }
-
- // // Check if target dataset exists and is published
- // const targetDataset = await Dataset.query()
- // .where('publish_id', targetDatasetPublish)
- // .where('server_state', 'published')
- // .preload('identifier')
- // .first();
- // Check if target dataset exists and is published by querying via identifier
- const targetDataset = await Dataset.query()
- .where('server_state', 'published')
- .whereHas('identifier', (query) => {
- query.where('value', doi);
- })
- .preload('identifier')
- .first();
-
- if (!targetDataset) {
- if (this.verbose) {
- this.logger.warning(`โ ๏ธ Target dataset with publish_id ${doi} not found or not published`);
- }
- continue;
- }
-
- // Ensure we have a valid source dataset with proper preloading
- if (!reference.dataset) {
- this.logger.warning(`โ ๏ธ Source dataset ${reference.document_id} not properly loaded, skipping...`);
- continue;
- }
-
- // Check if reverse reference exists
- const reverseReferenceExists = await this.checkReverseReferenceExists(
- targetDataset.id,
- reference.document_id,
- reference.relation,
- reference.dataset.identifier.value
- );
-
- if (!reverseReferenceExists) {
- const reverseRelation = this.getReverseRelation(reference.relation);
- if (reverseRelation) {
- // Only add if we have a valid reverse relation
- missingReferences.push({
- sourceDatasetId: reference.document_id,
- targetDatasetId: targetDataset.id,
- sourcePublishId: reference.dataset.publish_id || null,
- targetPublishId: targetDataset.publish_id || null,
- referenceType: reference.type,
- relation: reference.relation,
- doi: reference.value,
- reverseRelation: reverseRelation,
- sourceDoi: reference.dataset.identifier ? reference.dataset.identifier.value : null,
- targetDoi: targetDataset.identifier ? targetDataset.identifier.value : null,
- sourceReferenceLabel: reference.label || null,
- });
- }
- }
- }
-
- this.logger.info(`โ
Processed ${processedCount} references (${skippedCount} skipped due to relation filtering)`);
- return missingReferences;
- }
-
- private extractDoiFromReference(reference: string): string | null {
- // Match DOI pattern, with or without URL prefix
- const doiPattern = /(?:https?:\/\/)?(?:doi\.org\/)?(.+)/i;
- const match = reference.match(doiPattern);
-
- if (match && match[1]) {
- return match[1]; // Returns just "10.24341/tethys.99.2"
- }
-
- return null;
- }
-
- private extractDatasetPublishIdFromReference(value: string): number | null {
- // Extract from DOI: https://doi.org/10.24341/tethys.107 -> 107
- const doiMatch = value.match(/10\.24341\/tethys\.(\d+)/);
- if (doiMatch) {
- return parseInt(doiMatch[1]);
- }
-
- // Extract from URL: https://tethys.at/dataset/107 -> 107
- const urlMatch = value.match(/tethys\.at\/dataset\/(\d+)/);
- if (urlMatch) {
- return parseInt(urlMatch[1]);
- }
-
- return null;
- }
-
- private async checkReverseReferenceExists(
- targetDatasetId: number,
- sourceDatasetId: number,
- originalRelation: string,
- sourceDatasetIdentifier: string | null,
- ): Promise {
- const reverseRelation = this.getReverseRelation(originalRelation);
-
- if (!reverseRelation) {
- return true; // If no reverse relation is defined, consider it as "exists" to skip processing
- }
-
- // Only check for reverse references where the source dataset is also published
- const reverseReference = await DatasetReference.query()
- // We don't filter by source document_id here to find any incoming reference from any published dataset
- .where('document_id', targetDatasetId)
- // .where('related_document_id', sourceDatasetId) // Ensure it's an incoming reference
- .where('relation', reverseRelation)
- .where('value', 'like', `%${sourceDatasetIdentifier}`) // Basic check to ensure it points back to source dataset
- .first();
-
- return !!reverseReference;
- }
-
- private getReverseRelation(relation: string): string | null {
- const relationMap: Record = {
- IsNewVersionOf: 'IsPreviousVersionOf',
- IsPreviousVersionOf: 'IsNewVersionOf',
- IsVariantFormOf: 'IsOriginalFormOf',
- IsOriginalFormOf: 'IsVariantFormOf',
- Continues: 'IsContinuedBy',
- IsContinuedBy: 'Continues',
- HasPart: 'IsPartOf',
- IsPartOf: 'HasPart',
- };
-
- // Only return reverse relation if it exists in our map, otherwise return null
- return relationMap[relation] || null;
- }
-
- private printMissingReferencesList(missingReferences: MissingCrossReference[]) {
- console.log('โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ');
- console.log('โ MISSING CROSS-REFERENCES REPORT โ');
- console.log('โ (Published Datasets Only - Filtered Relations) โ');
- console.log('โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ');
- console.log();
-
- missingReferences.forEach((missing, index) => {
- console.log(
- `${index + 1}. Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId} Identifier: ${missing.sourceDoi})
- ${missing.relation} Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId} Identifier: ${missing.targetDoi})`,
- );
- console.log(` โโ Current relation: "${missing.relation}"`);
- console.log(` โโ Missing reverse relation: "${missing.reverseRelation}"`);
- console.log(` โโ Reference type: ${missing.referenceType}`);
- console.log(` โโ DOI/URL: ${missing.doi}`);
- console.log();
- });
-
- console.log('โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ');
- console.log(`โ SUMMARY: ${missingReferences.length} missing reverse reference(s) detected โ`);
- console.log(`โ Processed relations: ${this.ALLOWED_RELATIONS.join(', ')} โ`);
- console.log('โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ');
- }
-
- private async fixMissingReferences(missingReferences: MissingCrossReference[]) {
- this.logger.info('๐ง Creating missing cross-references in database...');
-
- let fixedCount = 0;
- let errorCount = 0;
-
- for (const [index, missing] of missingReferences.entries()) {
- try {
- // Get both source and target datasets
- const sourceDataset = await Dataset.query()
- .where('id', missing.sourceDatasetId)
- .where('server_state', 'published')
- .preload('identifier')
- .preload('titles') // Preload titles to get mainTitle
- .first();
-
- const targetDataset = await Dataset.query().where('id', missing.targetDatasetId).where('server_state', 'published').first();
-
- if (!sourceDataset) {
- this.logger.warning(`โ ๏ธ Source dataset ${missing.sourceDatasetId} not found or not published, skipping...`);
- errorCount++;
- continue;
- }
-
- if (!targetDataset) {
- this.logger.warning(`โ ๏ธ Target dataset ${missing.targetDatasetId} not found or not published, skipping...`);
- errorCount++;
- continue;
- }
-
- // **NEW: Update the original reference if related_document_id is missing**
- const originalReference = await DatasetReference.query()
- .where('document_id', missing.sourceDatasetId)
- .where('relation', missing.relation)
- .where('value', 'like', `%${missing.targetDoi}%`)
- .first();
- if (originalReference && !originalReference.related_document_id) {
- originalReference.related_document_id = missing.targetDatasetId;
- await originalReference.save();
- if (this.verbose) {
- this.logger.info(`๐ Updated original reference with related_document_id: ${missing.targetDatasetId}`);
- }
- }
-
- // Create the reverse reference using the referenced_by relationship
- // Example: If Dataset 297 IsNewVersionOf Dataset 144
- // We create an incoming reference for Dataset 144 that shows Dataset 297 IsPreviousVersionOf it
- const reverseReference = new DatasetReference();
- // Don't set document_id - this creates an incoming reference via related_document_id
- reverseReference.document_id = missing.targetDatasetId; //
- reverseReference.related_document_id = missing.sourceDatasetId;
- reverseReference.type = 'DOI';
- reverseReference.relation = missing.reverseRelation;
-
- // Use the source dataset's DOI for the value (what's being referenced)
- if (sourceDataset.identifier?.value) {
- reverseReference.value = `https://doi.org/${sourceDataset.identifier.value}`;
- } else {
- // Fallback to dataset URL if no DOI
- reverseReference.value = `https://tethys.at/dataset/${sourceDataset.publish_id || missing.sourceDatasetId}`;
- }
-
- // Use the source dataset's main title for the label
- //reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
- // get label of forward reference
- reverseReference.label = missing.sourceReferenceLabel || sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
- // reverseReference.notes = `Auto-created by detect:missing-cross-references command on ${DateTime.now().toISO()} to fix missing bidirectional reference.`;
-
- // Save the new reverse reference
- // Also save 'server_date_modified' on target dataset to trigger any downstream updates (e.g. search index)
- targetDataset.server_date_modified = DateTime.now();
- await targetDataset.save();
-
- await reverseReference.save();
- fixedCount++;
-
- if (this.verbose) {
- this.logger.info(
- `โ
[${index + 1}/${missingReferences.length}] Created reverse reference: Dataset ${missing.sourceDatasetId} -> ${missing.targetDatasetId} (${missing.reverseRelation})`,
- );
- } else if ((index + 1) % 10 === 0) {
- this.logger.info(`๐ Fixed ${fixedCount}/${missingReferences.length} references...`);
- }
- } catch (error) {
- this.logger.error(
- `โ Error creating reverse reference for datasets ${missing.targetDatasetId} -> ${missing.sourceDatasetId}:`,
- error,
- );
- errorCount++;
- }
- }
-
- this.logger.info(`๐ Fix completed: ${fixedCount} created, ${errorCount} errors`);
- }
-}
diff --git a/commands/index_datasets.ts b/commands/index_datasets.ts
index 322d4b8..ee76268 100644
--- a/commands/index_datasets.ts
+++ b/commands/index_datasets.ts
@@ -4,7 +4,7 @@
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import { create } from 'xmlbuilder2';
import Dataset from '#models/dataset';
-import XmlModel from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
import { readFileSync } from 'fs';
import SaxonJS from 'saxon-js';
import { Client } from '@opensearch-project/opensearch';
@@ -12,8 +12,10 @@ import { getDomain } from '#app/utils/utility-functions';
import { BaseCommand, flags } from '@adonisjs/core/ace';
import { CommandOptions } from '@adonisjs/core/types/ace';
import env from '#start/env';
+// import db from '@adonisjs/lucid/services/db';
+// import { default as Dataset } from '#models/dataset';
import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
+
const opensearchNode = env.get('OPENSEARCH_HOST', 'localhost');
const client = new Client({ node: `${opensearchNode}` }); // replace with your OpenSearch endpoint
@@ -28,10 +30,11 @@ export default class IndexDatasets extends BaseCommand {
public publish_id: number;
public static options: CommandOptions = {
- startApp: true, // Ensures the IoC container is ready to use
- staysAlive: false, // Command exits after running
+ startApp: true,
+ staysAlive: false,
};
+
async run() {
logger.debug('Hello world!');
// const { default: Dataset } = await import('#models/dataset');
@@ -41,12 +44,10 @@ export default class IndexDatasets extends BaseCommand {
const index_name = 'tethys-records';
for (var dataset of datasets) {
- const shouldUpdate = await this.shouldUpdateDataset(dataset, index_name);
- if (shouldUpdate) {
- await this.indexDocument(dataset, index_name, proc);
- } else {
- logger.info(`Dataset with publish_id ${dataset.publish_id} is up to date, skipping indexing`);
- }
+ // Logger.info(`File publish_id ${dataset.publish_id}`);
+ // const jsonString = await this.getJsonString(dataset, proc);
+ // console.log(jsonString);
+ await this.indexDocument(dataset, index_name, proc);
}
}
@@ -64,46 +65,6 @@ export default class IndexDatasets extends BaseCommand {
return await query.exec();
}
- private async shouldUpdateDataset(dataset: Dataset, index_name: string): Promise {
- try {
- // Check if publish_id exists before proceeding
- if (!dataset.publish_id) {
- // Return true to update since document doesn't exist in OpenSearch yet
- return true;
- }
- // Get the existing document from OpenSearch
- const response = await client.get({
- index: index_name,
- id: dataset.publish_id?.toString(),
- });
-
- const existingDoc = response.body._source;
-
- // Compare server_date_modified
- if (existingDoc && existingDoc.server_date_modified) {
- // Convert Unix timestamp (seconds) to milliseconds for DateTime.fromMillis()
- const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000);
- const currentModified = dataset.server_date_modified;
-
- // Only update if the dataset has been modified more recently
- if (currentModified <= existingModified) {
- return false;
- }
- }
-
- return true;
- } catch (error) {
- // If document doesn't exist or other error, we should index it
- if (error.statusCode === 404) {
- logger.info(`Dataset with publish_id ${dataset.publish_id} not found in index, will create new document`);
- return true;
- }
-
- logger.warn(`Error checking existing document for publish_id ${dataset.publish_id}: ${error.message}`);
- return true; // Index anyway if we can't determine the status
- }
- }
-
private async indexDocument(dataset: Dataset, index_name: string, proc: Buffer): Promise {
try {
const doc = await this.getJsonString(dataset, proc);
@@ -117,8 +78,7 @@ export default class IndexDatasets extends BaseCommand {
});
logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
} catch (error) {
- logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.
- Error: ${error.message}`);
+ logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.`);
}
}
@@ -151,16 +111,19 @@ export default class IndexDatasets extends BaseCommand {
}
private async getDatasetXmlDomNode(dataset: Dataset): Promise {
- const serializer = new XmlModel(dataset).enableCaching().excludeEmptyFields();
+ const xmlModel = new XmlModel(dataset);
// xmlModel.setModel(dataset);
-
+ xmlModel.excludeEmptyFields();
+ xmlModel.caching = true;
+ // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+ // dataset.load('xmlCache');
if (dataset.xmlCache) {
- serializer.setCache(dataset.xmlCache);
+ xmlModel.xmlCache = dataset.xmlCache;
}
- // return cache.toXmlDocument();
- const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
- return xmlDocument;
+ // return cache.getDomDocument();
+ const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+ return domDocument;
}
private addSpecInformation(domNode: XMLBuilder, information: string) {
diff --git a/commands/list_updatable_datacite.ts b/commands/list_updatable_datacite.ts
deleted file mode 100644
index aed411a..0000000
--- a/commands/list_updatable_datacite.ts
+++ /dev/null
@@ -1,346 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command list-updateable-datacite
-| DONE: create commands/list_updeatable_datacite.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import { CommandOptions } from '@adonisjs/core/types/ace';
-import Dataset from '#models/dataset';
-import { DoiClient } from '#app/Library/Doi/DoiClient';
-import env from '#start/env';
-import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
-import pLimit from 'p-limit';
-
-export default class ListUpdateableDatacite extends BaseCommand {
- static commandName = 'list:updateable-datacite';
- static description = 'List all datasets that need DataCite DOI updates';
-
- public static needsApplication = true;
-
- // private chunkSize = 100; // Set chunk size for pagination
-
- @flags.boolean({ alias: 'v', description: 'Verbose output showing detailed information' })
- public verbose: boolean = false;
-
- @flags.boolean({ alias: 'c', description: 'Show only count of updatable datasets' })
- public countOnly: boolean = false;
-
- @flags.boolean({ alias: 'i', description: 'Show only publish IDs (useful for scripting)' })
- public idsOnly: boolean = false;
-
- @flags.number({ description: 'Chunk size for processing datasets (default: 50)' })
- public chunkSize: number = 50;
-
- //example: node ace list:updateable-datacite
- //example: node ace list:updateable-datacite --verbose
- //example: node ace list:updateable-datacite --count-only
- //example: node ace list:updateable-datacite --ids-only
- //example: node ace list:updateable-datacite --chunk-size 50
-
- public static options: CommandOptions = {
- startApp: true,
- stayAlive: false,
- };
-
- async run() {
- const prefix = env.get('DATACITE_PREFIX', '');
- const base_domain = env.get('BASE_DOMAIN', '');
-
- if (!prefix || !base_domain) {
- logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables');
- return;
- }
-
- // Prevent conflicting flags
- if ((this.verbose && this.countOnly) || (this.verbose && this.idsOnly)) {
- logger.error('Flags --verbose cannot be combined with --count-only or --ids-only');
- return;
- }
-
- const chunkSize = this.chunkSize || 50;
- let page = 1;
- let hasMoreDatasets = true;
- let totalProcessed = 0;
- const updatableDatasets: Dataset[] = [];
-
- if (!this.countOnly && !this.idsOnly) {
- logger.info(`Processing datasets in chunks of ${chunkSize}...`);
- }
-
- while (hasMoreDatasets) {
- const datasets = await this.getDatasets(page, chunkSize);
-
- if (datasets.length === 0) {
- hasMoreDatasets = false;
- break;
- }
-
- if (!this.countOnly && !this.idsOnly) {
- logger.info(`Processing chunk ${page} (${datasets.length} datasets)...`);
- }
-
- const chunkUpdatableDatasets = await this.processChunk(datasets);
- updatableDatasets.push(...chunkUpdatableDatasets);
- totalProcessed += datasets.length;
-
- page += 1;
- if (datasets.length < chunkSize) {
- hasMoreDatasets = false;
- }
- }
-
- if (!this.countOnly && !this.idsOnly) {
- logger.info(`Processed ${totalProcessed} datasets total, found ${updatableDatasets.length} that need updates`);
- }
-
- if (this.countOnly) {
- console.log(updatableDatasets.length);
- } else if (this.idsOnly) {
- updatableDatasets.forEach((dataset) => console.log(dataset.publish_id));
- } else if (this.verbose) {
- await this.showVerboseOutput(updatableDatasets);
- } else {
- this.showSimpleOutput(updatableDatasets);
- }
- }
-
- /**
- * Processes a chunk of datasets to determine which ones need DataCite updates
- *
- * This method handles parallel processing of datasets within a chunk, providing
- * efficient error handling and filtering of results.
- *
- * @param datasets - Array of Dataset objects to process
- * @returns Promise - Array of datasets that need updates
- */
- // private async processChunk(datasets: Dataset[]): Promise {
- // // Process datasets in parallel using Promise.allSettled for better error handling
- // //
- // // Why Promise.allSettled vs Promise.all?
- // // - Promise.all fails fast: if ANY promise rejects, the entire operation fails
- // // - Promise.allSettled waits for ALL promises: some can fail, others succeed
- // // - This is crucial for batch processing where we don't want one bad dataset
- // // to stop processing of the entire chunk
- // const results = await Promise.allSettled(
- // datasets.map(async (dataset) => {
- // try {
- // // Check if this specific dataset needs a DataCite update
- // const needsUpdate = await this.shouldUpdateDataset(dataset);
-
- // // Return the dataset if it needs update, null if it doesn't
- // // This creates a sparse array that we'll filter later
- // return needsUpdate ? dataset : null;
- // } catch (error) {
- // // Error handling for individual dataset checks
- // //
- // // Log warnings only if we're not in silent modes (count-only or ids-only)
- // // This prevents log spam when running automated scripts
- // if (!this.countOnly && !this.idsOnly) {
- // logger.warn(`Error checking dataset ${dataset.publish_id}: ${error.message}`);
- // }
-
- // // IMPORTANT DECISION: Return the dataset anyway if we can't determine status
- // //
- // // Why? It's safer to include a dataset that might not need updating
- // // than to miss one that actually does need updating. This follows the
- // // "fail-safe" principle - if we're unsure, err on the side of caution
- // return dataset;
- // }
- // }),
- // );
-
- // // Filter and extract results from Promise.allSettled response
- // //
- // // Promise.allSettled returns an array of objects with this structure:
- // // - { status: 'fulfilled', value: T } for successful promises
- // // - { status: 'rejected', reason: Error } for failed promises
- // //
- // // We need to:
- // // 1. Only get fulfilled results (rejected ones are already handled above)
- // // 2. Filter out null values (datasets that don't need updates)
- // // 3. Extract the actual Dataset objects from the wrapper
- // return results
- // .filter(
- // (result): result is PromiseFulfilledResult =>
- // // Type guard: only include fulfilled results that have actual values
- // // This filters out:
- // // - Rejected promises (shouldn't happen due to try/catch, but safety first)
- // // - Fulfilled promises that returned null (datasets that don't need updates)
- // result.status === 'fulfilled' && result.value !== null,
- // )
- // .map((result) => result.value!); // Extract the Dataset from the wrapper
- // // The ! is safe here because we filtered out null values above
- // }
-
- private async processChunk(datasets: Dataset[]): Promise {
- // Limit concurrency to avoid API flooding (e.g., max 5 at once)
- const limit = pLimit(5);
-
- const tasks = datasets.map((dataset) =>
- limit(async () => {
- try {
- const needsUpdate = await this.shouldUpdateDataset(dataset);
- return needsUpdate ? dataset : null;
- } catch (error) {
- if (!this.countOnly && !this.idsOnly) {
- logger.warn(
- `Error checking dataset ${dataset.publish_id}: ${
- error instanceof Error ? error.message : JSON.stringify(error)
- }`,
- );
- }
- // Fail-safe: include dataset if uncertain
- return dataset;
- }
- }),
- );
-
- const results = await Promise.allSettled(tasks);
-
- return results
- .filter((result): result is PromiseFulfilledResult => result.status === 'fulfilled' && result.value !== null)
- .map((result) => result.value!);
- }
-
- private async getDatasets(page: number, chunkSize: number): Promise {
- return await Dataset.query()
- .orderBy('publish_id', 'asc')
- .preload('identifier')
- .preload('xmlCache')
- .preload('titles')
- .where('server_state', 'published')
- .whereHas('identifier', (identifierQuery) => {
- identifierQuery.where('type', 'doi');
- })
- .forPage(page, chunkSize); // Get files for the current page
- }
-
- private async shouldUpdateDataset(dataset: Dataset): Promise {
- try {
- let doiIdentifier = dataset.identifier;
- if (!doiIdentifier) {
- await dataset.load('identifier');
- doiIdentifier = dataset.identifier;
- }
-
- if (!doiIdentifier || doiIdentifier.type !== 'doi') {
- return false;
- }
-
- const datasetModified =
- dataset.server_date_modified instanceof DateTime
- ? dataset.server_date_modified
- : DateTime.fromJSDate(dataset.server_date_modified);
-
- if (!datasetModified) {
- return true;
- }
-
- if (datasetModified > DateTime.now()) {
- return false;
- }
-
- const doiClient = new DoiClient();
- const DOI_CHECK_TIMEOUT = 300; // ms
-
- const doiLastModified = await Promise.race([
- doiClient.getDoiLastModified(doiIdentifier.value),
- this.createTimeoutPromise(DOI_CHECK_TIMEOUT),
- ]).catch(() => null);
-
- if (!doiLastModified) {
- // If uncertain, better include dataset for update
- return true;
- }
-
- const doiModified = DateTime.fromJSDate(doiLastModified);
- if (datasetModified > doiModified) {
- const diffInSeconds = Math.abs(datasetModified.diff(doiModified, 'seconds').seconds);
- const toleranceSeconds = 600;
- return diffInSeconds > toleranceSeconds;
- }
- return false;
- } catch (error) {
- return true; // safer: include dataset if unsure
- }
- }
-
- /**
- * Create a timeout promise for API calls
- */
- private createTimeoutPromise(timeoutMs: number): Promise {
- return new Promise((_, reject) => {
- setTimeout(() => reject(new Error(`API call timeout after ${timeoutMs}ms`)), timeoutMs);
- });
- }
-
- private showSimpleOutput(updatableDatasets: Dataset[]): void {
- if (updatableDatasets.length === 0) {
- console.log('No datasets need DataCite updates.');
- return;
- }
-
- console.log(`\nFound ${updatableDatasets.length} dataset(s) that need DataCite updates:\n`);
-
- updatableDatasets.forEach((dataset) => {
- console.log(`publish_id ${dataset.publish_id} needs update - ${dataset.mainTitle || 'Untitled'}`);
- });
-
- console.log(`\nTo update these datasets, run:`);
- console.log(` node ace update:datacite`);
- console.log(`\nOr update specific datasets:`);
- console.log(` node ace update:datacite -p `);
- }
-
- private async showVerboseOutput(updatableDatasets: Dataset[]): Promise {
- if (updatableDatasets.length === 0) {
- console.log('No datasets need DataCite updates.');
- return;
- }
-
- console.log(`\nFound ${updatableDatasets.length} dataset(s) that need DataCite updates:\n`);
-
- for (const dataset of updatableDatasets) {
- await this.showDatasetDetails(dataset);
- }
-
- console.log(`\nSummary: ${updatableDatasets.length} datasets need updates`);
- }
-
- private async showDatasetDetails(dataset: Dataset): Promise {
- try {
- let doiIdentifier = dataset.identifier;
-
- if (!doiIdentifier) {
- await dataset.load('identifier');
- doiIdentifier = dataset.identifier;
- }
-
- const doiValue = doiIdentifier?.value || 'N/A';
- const datasetModified = dataset.server_date_modified;
-
- // Get DOI info from DataCite
- const doiClient = new DoiClient();
- const doiLastModified = await doiClient.getDoiLastModified(doiValue);
- const doiState = await doiClient.getDoiState(doiValue);
-
- console.log(`โโ Dataset ${dataset.publish_id} โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ`);
- console.log(`โ Title: ${dataset.mainTitle || 'Untitled'}`);
- console.log(`โ DOI: ${doiValue}`);
- console.log(`โ DOI State: ${doiState || 'Unknown'}`);
- console.log(`โ Dataset Modified: ${datasetModified ? datasetModified.toISO() : 'N/A'}`);
- console.log(`โ DOI Modified: ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'}`);
- console.log(`โ Status: NEEDS UPDATE`);
- console.log(`โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ\n`);
- } catch (error) {
- console.log(`โโ Dataset ${dataset.publish_id} โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ`);
- console.log(`โ Title: ${dataset.mainTitle || 'Untitled'}`);
- console.log(`โ DOI: ${dataset.identifier?.value || 'N/A'}`);
- console.log(`โ Error: ${error.message}`);
- console.log(`โ Status: NEEDS UPDATE (Error checking)`);
- console.log(`โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ\n`);
- }
- }
-}
diff --git a/commands/update_datacite.ts b/commands/update_datacite.ts
deleted file mode 100644
index 7ccb0f0..0000000
--- a/commands/update_datacite.ts
+++ /dev/null
@@ -1,266 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command update-datacite
-| DONE: create commands/update_datacite.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import { CommandOptions } from '@adonisjs/core/types/ace';
-import Dataset from '#models/dataset';
-import { DoiClient } from '#app/Library/Doi/DoiClient';
-import DoiClientException from '#app/exceptions/DoiClientException';
-import Index from '#app/Library/Utils/Index';
-import env from '#start/env';
-import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
-import { getDomain } from '#app/utils/utility-functions';
-
-export default class UpdateDatacite extends BaseCommand {
- static commandName = 'update:datacite';
- static description = 'Update DataCite DOI records for published datasets';
-
- public static needsApplication = true;
-
- @flags.number({ alias: 'p', description: 'Specific publish_id to update' })
- public publish_id: number;
-
- @flags.boolean({ alias: 'f', description: 'Force update all records regardless of modification date' })
- public force: boolean = false;
-
- @flags.boolean({ alias: 'd', description: 'Dry run - show what would be updated without making changes' })
- public dryRun: boolean = false;
-
- @flags.boolean({ alias: 's', description: 'Show detailed stats for each dataset that needs updating' })
- public stats: boolean = false;
-
- //example: node ace update:datacite -p 123 --force --dry-run
-
- public static options: CommandOptions = {
- startApp: true, // Whether to boot the application before running the command
- stayAlive: false, // Whether to keep the process alive after the command has executed
- };
-
- async run() {
- logger.info('Starting DataCite update process...');
-
- const prefix = env.get('DATACITE_PREFIX', '');
- const base_domain = env.get('BASE_DOMAIN', '');
- const apiUrl = env.get('DATACITE_API_URL', 'https://api.datacite.org');
-
- if (!prefix || !base_domain) {
- logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables');
- return;
- }
-
- logger.info(`Using DataCite API: ${apiUrl}`);
-
- const datasets = await this.getDatasets();
- logger.info(`Found ${datasets.length} datasets to process`);
-
- let updated = 0;
- let skipped = 0;
- let errors = 0;
-
- for (const dataset of datasets) {
- try {
- const shouldUpdate = this.force || (await this.shouldUpdateDataset(dataset));
-
- if (this.stats) {
- // Stats mode: show detailed information for datasets that need updating
- if (shouldUpdate) {
- await this.showDatasetStats(dataset);
- updated++;
- } else {
- skipped++;
- }
- continue;
- }
-
- if (!shouldUpdate) {
- logger.info(`Dataset ${dataset.publish_id}: Up to date, skipping`);
- skipped++;
- continue;
- }
-
- if (this.dryRun) {
- logger.info(`Dataset ${dataset.publish_id}: Would update DataCite record (dry run)`);
- updated++;
- continue;
- }
-
- await this.updateDataciteRecord(dataset, prefix, base_domain);
- logger.info(`Dataset ${dataset.publish_id}: Successfully updated DataCite record`);
- updated++;
- } catch (error) {
- logger.error(`Dataset ${dataset.publish_id}: Failed to update - ${error.message}`);
- errors++;
- }
- }
-
- if (this.stats) {
- logger.info(`\nDataCite Stats Summary: ${updated} datasets need updating, ${skipped} are up to date`);
- } else {
- logger.info(`DataCite update completed. Updated: ${updated}, Skipped: ${skipped}, Errors: ${errors}`);
- }
- }
-
- private async getDatasets(): Promise {
- const query = Dataset.query()
- .preload('identifier')
- .preload('xmlCache')
- .where('server_state', 'published')
- .whereHas('identifier', (identifierQuery) => {
- identifierQuery.where('type', 'doi');
- });
-
- if (this.publish_id) {
- query.where('publish_id', this.publish_id);
- }
-
- return await query.exec();
- }
-
- private async shouldUpdateDataset(dataset: Dataset): Promise {
- try {
- let doiIdentifier = dataset.identifier;
-
- if (!doiIdentifier) {
- await dataset.load('identifier');
- doiIdentifier = dataset.identifier;
- }
-
- if (!doiIdentifier || doiIdentifier.type !== 'doi') {
- return false;
- }
-
- const datasetModified = dataset.server_date_modified;
- const now = DateTime.now();
-
- if (!datasetModified) {
- return true; // Update if modification date is missing
- }
-
- if (datasetModified > now) {
- return false; // Skip invalid future dates
- }
-
- // Check DataCite DOI modification date
- const doiClient = new DoiClient();
- const doiLastModified = await doiClient.getDoiLastModified(doiIdentifier.value);
-
- if (!doiLastModified) {
- return false; // not Update if we can't get DOI info
- }
-
- const doiModified = DateTime.fromJSDate(doiLastModified);
- if (datasetModified > doiModified) {
- // if dataset was modified after DOI creation
- // Calculate the difference in seconds
- const diffInSeconds = Math.abs(datasetModified.diff(doiModified, 'seconds').seconds);
-
- // Define tolerance threshold (60 seconds = 1 minute)
- const toleranceSeconds = 60;
-
- // Only update if the difference is greater than the tolerance
- // This prevents unnecessary updates for minor timestamp differences
- return diffInSeconds > toleranceSeconds;
- } else {
- return false; // No update needed
- }
- } catch (error) {
- return false; // not update if we can't determine status or other error
- }
- }
-
- private async updateDataciteRecord(dataset: Dataset, prefix: string, base_domain: string): Promise {
- try {
- // Get the DOI identifier (HasOne relationship)
- let doiIdentifier = dataset.identifier;
-
- if (!doiIdentifier) {
- await dataset.load('identifier');
- doiIdentifier = dataset.identifier;
- }
-
- if (!doiIdentifier || doiIdentifier.type !== 'doi') {
- throw new Error('No DOI identifier found for dataset');
- }
-
- // Generate XML metadata
- const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
- if (!xmlMeta) {
- throw new Error('Failed to generate XML metadata');
- }
-
- // Construct DOI value and landing page URL
- const doiValue = doiIdentifier.value; // Use existing DOI value
- const landingPageUrl = `https://doi.${getDomain(base_domain)}/${doiValue}`;
-
- // Update DataCite record
- const doiClient = new DoiClient();
- const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);
-
- if (dataciteResponse?.status === 201) {
- // // Update dataset modification date
- // dataset.server_date_modified = DateTime.now();
- // await dataset.save();
-
- // // Update search index
- // const index_name = 'tethys-records';
- // await Index.indexDocument(dataset, index_name);
-
- logger.debug(`Dataset ${dataset.publish_id}: DataCite record and search index updated successfully`);
- } else {
- throw new DoiClientException(
- dataciteResponse?.status || 500,
- `Unexpected DataCite response code: ${dataciteResponse?.status}`,
- );
- }
- } catch (error) {
- if (error instanceof DoiClientException) {
- throw error;
- }
- throw new Error(`Failed to update DataCite record: ${error.message}`);
- }
- }
-
- /**
- * Shows detailed statistics for a dataset that needs updating
- */
- private async showDatasetStats(dataset: Dataset): Promise {
- try {
- let doiIdentifier = dataset.identifier;
-
- if (!doiIdentifier) {
- await dataset.load('identifier');
- doiIdentifier = dataset.identifier;
- }
-
- const doiValue = doiIdentifier?.value || 'N/A';
- const doiStatus = doiIdentifier?.status || 'N/A';
- const datasetModified = dataset.server_date_modified;
-
- // Get DOI info from DataCite
- const doiClient = new DoiClient();
- const doiLastModified = await doiClient.getDoiLastModified(doiValue);
- const doiState = await doiClient.getDoiState(doiValue);
-
- console.log(`
- โโ Dataset ${dataset.publish_id} โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
- โ DOI Value: ${doiValue}
- โ DOI Status (DB): ${doiStatus}
- โ DOI State (DataCite): ${doiState || 'Unknown'}
- โ Dataset Modified: ${datasetModified ? datasetModified.toISO() : 'N/A'}
- โ DOI Modified: ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'}
- โ Needs Update: YES - Dataset newer than DOI
- โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ`);
- } catch (error) {
- console.log(`
- โโ Dataset ${dataset.publish_id} โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
- โ DOI Value: ${dataset.identifier?.value || 'N/A'}
- โ Error: ${error.message}
- โ Needs Update: YES - Error checking status
- โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ`);
- }
- }
-}
diff --git a/components.d.ts b/components.d.ts
index 001762d..3834bf1 100644
--- a/components.d.ts
+++ b/components.d.ts
@@ -11,21 +11,3 @@ declare module '@vue/runtime-core' {
NInput: (typeof import('naive-ui'))['NInput'];
}
}
-
-// types/leaflet-src-dom-DomEvent.d.ts
-declare module 'leaflet/src/dom/DomEvent' {
- export type DomEventHandler = (e?: any) => void;
-
- // Attach event listeners. `obj` can be any DOM node or object with event handling.
- export function on(obj: any, types: string, fn: DomEventHandler, context?: any): void;
-
- // Detach event listeners.
- export function off(obj: any, types: string, fn?: DomEventHandler, context?: any): void;
-
- // Prevent default on native events
- export function preventDefault(ev?: Event | undefined): void;
-
- // Optional: other helpers you might need later
- export function stopPropagation(ev?: Event | undefined): void;
- export function stop(ev?: Event | undefined): void;
-}
\ No newline at end of file
diff --git a/config/mail.ts b/config/mail.ts
index a97489f..8016c29 100644
--- a/config/mail.ts
+++ b/config/mail.ts
@@ -16,7 +16,7 @@ const mailConfig = defineConfig({
host: env.get('SMTP_HOST', ''),
port: env.get('SMTP_PORT'),
secure: false,
- ignoreTLS: true,
+ // ignoreTLS: true,
requireTLS: false,
/**
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 10d0f37..8ef61c7 100644
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -1,74 +1,47 @@
#!/bin/bash
+
+# # Run freshclam to update virus definitions
+# freshclam
+
+# # Sleep for a few seconds to give ClamAV time to start
+# sleep 5
+
+# # Start the ClamAV daemon
+# /etc/init.d/clamav-daemon start
+
+# bootstrap clam av service and clam av database updater
set -m
-echo "Starting ClamAV services..."
+function process_file() {
+ if [[ ! -z "$1" ]]; then
+ local SETTING_LIST=$(echo "$1" | tr ',' '\n' | grep "^[A-Za-z][A-Za-z]*=.*$")
+ local SETTING
+
+ for SETTING in ${SETTING_LIST}; do
+ # Remove any existing copies of this setting. We do this here so that
+ # settings with multiple values (e.g. ExtraDatabase) can still be added
+ # multiple times below
+ local KEY=${SETTING%%=*}
+ sed -i $2 -e "/^${KEY} /d"
+ done
+ for SETTING in ${SETTING_LIST}; do
+ # Split on first '='
+ local KEY=${SETTING%%=*}
+ local VALUE=${SETTING#*=}
+ echo "${KEY} ${VALUE}" >> "$2"
+ done
+ fi
+}
-# Try to download database if missing
-# if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then
-# echo "Downloading ClamAV database (this may take a while)..."
-
-# # Simple freshclam run without complex config
-# if freshclam --datadir=/var/lib/clamav --quiet; then
-# echo "โ Database downloaded successfully"
-# else
-# echo "โ Database download failed - creating minimal setup"
-# # Create a dummy file so clamd doesn't immediately fail
-# touch /var/lib/clamav/.dummy
-# fi
-# fi
-
-# Start freshclam daemon for automatic updates
-echo "Starting freshclam daemon for automatic updates..."
-# sg clamav -c "freshclam -d" &
-# Added --daemon-notify to freshclam - This notifies clamd when the database updates
-freshclam -d --daemon-notify=/etc/clamav/clamd.conf &
-#freshclam -d &
+# process_file "${CLAMD_SETTINGS_CSV}" /etc/clamav/clamd.conf
+# process_file "${FRESHCLAM_SETTINGS_CSV}" /etc/clamav/freshclam.conf
+# start in background
+freshclam -d &
# /etc/init.d/clamav-freshclam start &
-# Start clamd in background
-# Start clamd in foreground (so dumb-init can supervise it)
+clamd
# /etc/init.d/clamav-daemon start &
-# Give freshclam a moment to start
-sleep 2
-
-# Start clamd daemon in background using sg
-echo "Starting ClamAV daemon..."
-# sg clamav -c "clamd" &
-# Use sg to run clamd with proper group permissions
-# sg clamav -c "clamd" &
-# clamd --config-file=/etc/clamav/clamd.conf &
-clamd &
-
-
-# Give services time to start
-echo "Waiting for services to initialize..."
-sleep 8
-
-# simple check
-if pgrep clamd > /dev/null; then
- echo "โ ClamAV daemon is running"
-else
- echo "โ ClamAV daemon status uncertain, but continuing..."
-fi
-
-# Check if freshclam daemon is running
-if pgrep freshclam > /dev/null; then
- echo "โ Freshclam daemon is running"
-else
- echo "โ Freshclam daemon status uncertain, but continuing..."
-fi
-
-# # Optional: Test socket connectivity
-# if [ -S /var/run/clamav/clamd.socket ]; then
-# echo "โ ClamAV socket exists"
-# else
-# echo "โ WARNING: ClamAV socket not found - services may still be starting"
-# fi
-
-# # change back to CMD of dockerfile
-echo "โ ClamAV setup complete"
-echo "Starting main application..."
-# exec dumb-init -- "$@"
+# change back to CMD of dockerfile
exec "$@"
\ No newline at end of file
diff --git a/docs/commands/index-datasets.md b/docs/commands/index-datasets.md
deleted file mode 100644
index baecfe6..0000000
--- a/docs/commands/index-datasets.md
+++ /dev/null
@@ -1,278 +0,0 @@
-# Dataset Indexing Command
-
-AdonisJS Ace command for indexing and synchronizing published datasets with OpenSearch for search functionality.
-
-## Overview
-
-The `index:datasets` command processes published datasets and creates/updates corresponding search index documents in OpenSearch. It intelligently compares modification timestamps to only re-index datasets when necessary, optimizing performance while maintaining search index accuracy.
-
-## Command Syntax
-
-```bash
-node ace index:datasets [options]
-```
-
-## Options
-
-| Flag | Alias | Description |
-|------|-------|-------------|
-| `--publish_id ` | `-p` | Index a specific dataset by publish_id |
-
-## Usage Examples
-
-### Basic Operations
-
-```bash
-# Index all published datasets that have been modified since last indexing
-node ace index:datasets
-
-# Index a specific dataset by publish_id
-node ace index:datasets --publish_id 231
-node ace index:datasets -p 231
-```
-
-## How It Works
-
-### 1. **Dataset Selection**
-The command processes datasets that meet these criteria:
-- `server_state = 'published'` - Only published datasets
-- Has preloaded `xmlCache` relationship for metadata transformation
-- Optionally filtered by specific `publish_id`
-
-### 2. **Smart Update Detection**
-For each dataset, the command:
-- Checks if the dataset exists in the OpenSearch index
-- Compares `server_date_modified` timestamps
-- Only re-indexes if the dataset is newer than the indexed version
-
-### 3. **Document Processing**
-The indexing process involves:
-1. **XML Generation**: Creates structured XML from dataset metadata
-2. **XSLT Transformation**: Converts XML to JSON using Saxon-JS processor
-3. **Index Update**: Updates or creates the document in OpenSearch
-4. **Logging**: Records success/failure for each operation
-
-## Index Structure
-
-### Index Configuration
-- **Index Name**: `tethys-records`
-- **Document ID**: Dataset `publish_id`
-- **Refresh**: `true` (immediate availability)
-
-### Document Fields
-The indexed documents contain:
-- **Metadata Fields**: Title, description, authors, keywords
-- **Identifiers**: DOI, publish_id, and other identifiers
-- **Temporal Data**: Publication dates, coverage periods
-- **Geographic Data**: Spatial coverage information
-- **Technical Details**: Data formats, access information
-- **Timestamps**: Creation and modification dates
-
-## Example Output
-
-### Successful Run
-```bash
-node ace index:datasets
-```
-```
-Found 150 published datasets to process
-Dataset with publish_id 231 successfully indexed
-Dataset with publish_id 245 is up to date, skipping indexing
-Dataset with publish_id 267 successfully indexed
-An error occurred while indexing dataset with publish_id 289. Error: Invalid XML metadata
-Processing completed: 148 indexed, 1 skipped, 1 error
-```
-
-### Specific Dataset
-```bash
-node ace index:datasets --publish_id 231
-```
-```
-Found 1 published dataset to process
-Dataset with publish_id 231 successfully indexed
-Processing completed: 1 indexed, 0 skipped, 0 errors
-```
-
-## Update Logic
-
-The command uses intelligent indexing to avoid unnecessary processing:
-
-| Condition | Action | Reason |
-|-----------|--------|--------|
-| Dataset not in index | โ
Index | New dataset needs indexing |
-| Dataset newer than indexed version | โ
Re-index | Dataset has been updated |
-| Dataset same/older than indexed version | โ Skip | Already up to date |
-| OpenSearch document check fails | โ
Index | Better safe than sorry |
-| Invalid XML metadata | โ Skip + Log Error | Cannot process invalid data |
-
-### Timestamp Comparison
-```typescript
-// Example comparison logic
-const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000);
-const currentModified = dataset.server_date_modified;
-
-if (currentModified <= existingModified) {
- // Skip - already up to date
- return false;
-}
-// Proceed with indexing
-```
-
-## XML Transformation Process
-
-### 1. **XML Generation**
-```xml
-
-
-
-
- Research Dataset Title
- Dataset description...
-
-
-
-```
-
-### 2. **XSLT Processing**
-The command uses Saxon-JS with a compiled stylesheet (`solr.sef.json`) to transform XML to JSON:
-```javascript
-const result = await SaxonJS.transform({
- stylesheetText: proc,
- destination: 'serialized',
- sourceText: xmlString,
-});
-```
-
-### 3. **Final JSON Document**
-```json
-{
- "id": "231",
- "title": "Research Dataset Title",
- "description": "Dataset description...",
- "authors": ["Author Name"],
- "server_date_modified": 1634567890,
- "publish_id": 231
-}
-```
-
-## Configuration Requirements
-
-### Environment Variables
-```bash
-# OpenSearch Configuration
-OPENSEARCH_HOST=localhost:9200
-
-# For production:
-# OPENSEARCH_HOST=your-opensearch-cluster:9200
-```
-
-### Required Files
-- **XSLT Stylesheet**: `public/assets2/solr.sef.json` - Compiled Saxon-JS stylesheet for XML transformation
-
-### Database Relationships
-The command expects these model relationships:
-```typescript
-// Dataset model must have:
-@hasOne(() => XmlCache, { foreignKey: 'dataset_id' })
-public xmlCache: HasOne
-```
-
-## Error Handling
-
-The command handles various error scenarios gracefully:
-
-### Common Errors and Solutions
-
-| Error | Cause | Solution |
-|-------|-------|----------|
-| `XSLT transformation failed` | Invalid XML or missing stylesheet | Check XML structure and stylesheet path |
-| `OpenSearch connection error` | Service unavailable | Verify OpenSearch is running and accessible |
-| `JSON parse error` | Malformed transformation result | Check XSLT stylesheet output format |
-| `Missing xmlCache relationship` | Data integrity issue | Ensure xmlCache exists for dataset |
-
-### Error Logging
-```bash
-# Typical error log entry
-An error occurred while indexing dataset with publish_id 231.
-Error: XSLT transformation failed: Invalid XML structure at line 15
-```
-
-## Performance Considerations
-
-### Batch Processing
-- Processes datasets sequentially to avoid overwhelming OpenSearch
-- Each dataset is committed individually for reliability
-- Failed indexing of one dataset doesn't stop processing others
-
-### Resource Usage
-- **Memory**: XML/JSON transformations require temporary memory
-- **Network**: OpenSearch API calls for each dataset
-- **CPU**: XSLT transformations are CPU-intensive
-
-### Optimization Tips
-```bash
-# Index only recently modified datasets (run regularly)
-node ace index:datasets
-
-# Index specific datasets when needed
-node ace index:datasets --publish_id 231
-
-# Consider running during off-peak hours for large batches
-```
-
-## Integration with Other Systems
-
-### Search Functionality
-The indexed documents power:
-- **Dataset Search**: Full-text search across metadata
-- **Faceted Browsing**: Filter by authors, keywords, dates
-- **Geographic Search**: Spatial query capabilities
-- **Auto-complete**: Suggest dataset titles and keywords
-
-### Related Commands
-- [`update:datacite`](update-datacite.md) - Often run after indexing to sync DOI metadata
-- **Database migrations** - May require re-indexing after schema changes
-
-### API Integration
-The indexed data is consumed by:
-- **Search API**: `/api/search` endpoints
-- **Browse API**: `/api/datasets` with filtering
-- **Recommendations**: Related dataset suggestions
-
-## Monitoring and Maintenance
-
-### Regular Tasks
-```bash
-# Daily indexing (recommended cron job)
-0 2 * * * cd /path/to/project && node ace index:datasets
-
-# Weekly full re-index (if needed)
-0 3 * * 0 cd /path/to/project && node ace index:datasets --force
-```
-
-### Health Checks
-- Monitor OpenSearch cluster health
-- Check for failed indexing operations in logs
-- Verify search functionality is working
-- Compare dataset counts between database and index
-
-### Troubleshooting
-```bash
-# Check specific dataset indexing
-node ace index:datasets --publish_id 231
-
-# Verify OpenSearch connectivity
-curl -X GET "localhost:9200/_cluster/health"
-
-# Check index statistics
-curl -X GET "localhost:9200/tethys-records/_stats"
-```
-
-## Best Practices
-
-1. **Regular Scheduling**: Run the command regularly (daily) to keep the search index current
-2. **Monitor Logs**: Watch for transformation errors or OpenSearch issues
-3. **Backup Strategy**: Include OpenSearch indices in backup procedures
-4. **Resource Management**: Monitor OpenSearch cluster resources during bulk operations
-5. **Testing**: Verify search functionality after major indexing operations
-6. **Coordination**: Run indexing before DataCite updates when both are needed
\ No newline at end of file
diff --git a/docs/commands/update-datacite.md b/docs/commands/update-datacite.md
deleted file mode 100644
index 06041f0..0000000
--- a/docs/commands/update-datacite.md
+++ /dev/null
@@ -1,216 +0,0 @@
-# DataCite Update Command
-
-AdonisJS Ace command for updating DataCite DOI records for published datasets.
-
-## Overview
-
-The `update:datacite` command synchronizes your local dataset metadata with DataCite DOI records. It intelligently compares modification dates to only update records when necessary, reducing unnecessary API calls and maintaining data consistency.
-
-## Command Syntax
-
-```bash
-node ace update:datacite [options]
-```
-
-## Options
-
-| Flag | Alias | Description |
-|------|-------|-------------|
-| `--publish_id ` | `-p` | Update a specific dataset by publish_id |
-| `--force` | `-f` | Force update all records regardless of modification date |
-| `--dry-run` | `-d` | Preview what would be updated without making changes |
-| `--stats` | `-s` | Show detailed statistics for datasets that need updating |
-
-## Usage Examples
-
-### Basic Operations
-
-```bash
-# Update all datasets that have been modified since their DOI was last updated
-node ace update:datacite
-
-# Update a specific dataset
-node ace update:datacite --publish_id 231
-node ace update:datacite -p 231
-
-# Force update all datasets with DOIs (ignores modification dates)
-node ace update:datacite --force
-```
-
-### Preview and Analysis
-
-```bash
-# Preview what would be updated (dry run)
-node ace update:datacite --dry-run
-
-# Show detailed statistics for datasets that need updating
-node ace update:datacite --stats
-
-# Show stats for a specific dataset
-node ace update:datacite --stats --publish_id 231
-```
-
-### Combined Options
-
-```bash
-# Dry run for a specific dataset
-node ace update:datacite --dry-run --publish_id 231
-
-# Show stats for all datasets (including up-to-date ones)
-node ace update:datacite --stats --force
-```
-
-## Command Modes
-
-### 1. **Normal Mode** (Default)
-Updates DataCite records for datasets that have been modified since their DOI was last updated.
-
-**Example Output:**
-```
-Using DataCite API: https://api.test.datacite.org
-Found 50 datasets to process
-Dataset 231: Successfully updated DataCite record
-Dataset 245: Up to date, skipping
-Dataset 267: Successfully updated DataCite record
-DataCite update completed. Updated: 15, Skipped: 35, Errors: 0
-```
-
-### 2. **Dry Run Mode** (`--dry-run`)
-Shows what would be updated without making any changes to DataCite.
-
-**Use Case:** Preview updates before running the actual command.
-
-**Example Output:**
-```
-Dataset 231: Would update DataCite record (dry run)
-Dataset 267: Would update DataCite record (dry run)
-Dataset 245: Up to date, skipping
-DataCite update completed. Updated: 2, Skipped: 1, Errors: 0
-```
-
-### 3. **Stats Mode** (`--stats`)
-Shows detailed information for each dataset that needs updating, including why it needs updating.
-
-**Use Case:** Debug synchronization issues, monitor dataset/DOI status, generate reports.
-
-**Example Output:**
-```
-โโ Dataset 231 โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
-โ DOI Value: 10.21388/tethys.231
-โ DOI Status (DB): findable
-โ DOI State (DataCite): findable
-โ Dataset Modified: 2024-09-15T10:30:00.000Z
-โ DOI Modified: 2024-09-10T08:15:00.000Z
-โ Needs Update: YES - Dataset newer than DOI
-โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
-
-โโ Dataset 267 โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
-โ DOI Value: 10.21388/tethys.267
-โ DOI Status (DB): findable
-โ DOI State (DataCite): findable
-โ Dataset Modified: 2024-09-18T14:20:00.000Z
-โ DOI Modified: 2024-09-16T12:45:00.000Z
-โ Needs Update: YES - Dataset newer than DOI
-โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
-
-DataCite Stats Summary: 2 datasets need updating, 48 are up to date
-```
-
-## Update Logic
-
-The command uses intelligent update detection:
-
-1. **Compares modification dates**: Dataset `server_date_modified` vs DOI last modification date from DataCite
-2. **Validates data integrity**: Checks for missing or future dates
-3. **Handles API failures gracefully**: Updates anyway if DataCite info can't be retrieved
-4. **Uses dual API approach**: DataCite REST API (primary) with MDS API fallback
-
-### When Updates Happen
-
-| Condition | Action | Reason |
-|-----------|--------|--------|
-| Dataset modified > DOI modified | โ
Update | Dataset has newer changes |
-| Dataset modified โค DOI modified | โ Skip | DOI is up to date |
-| Dataset date in future | โ Skip | Invalid data, needs investigation |
-| Dataset date missing | โ
Update | Can't determine staleness |
-| DataCite API error | โ
Update | Better safe than sorry |
-| `--force` flag used | โ
Update | Override all logic |
-
-## Environment Configuration
-
-Required environment variables:
-
-```bash
-# DataCite Credentials
-DATACITE_USERNAME=your_username
-DATACITE_PASSWORD=your_password
-
-# API Endpoints (environment-specific)
-DATACITE_API_URL=https://api.test.datacite.org # Test environment
-DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS
-
-DATACITE_API_URL=https://api.datacite.org # Production
-DATACITE_SERVICE_URL=https://mds.datacite.org # Production MDS
-
-# Project Configuration
-DATACITE_PREFIX=10.21388 # Your DOI prefix
-BASE_DOMAIN=tethys.at # Your domain
-```
-
-## Error Handling
-
-The command handles various error scenarios:
-
-- **Invalid modification dates**: Logs errors but continues processing other datasets
-- **DataCite API failures**: Falls back to MDS API, then to safe update
-- **Missing DOI identifiers**: Skips datasets without DOI identifiers
-- **Network issues**: Continues with next dataset after logging error
-
-## Integration
-
-The command integrates with:
-
-- **Dataset Model**: Uses `server_date_modified` for change detection
-- **DatasetIdentifier Model**: Reads DOI values and status
-- **OpenSearch Index**: Updates search index after DataCite update
-- **DoiClient**: Handles all DataCite API interactions
-
-## Common Workflows
-
-### Daily Maintenance
-```bash
-# Update any datasets modified today
-node ace update:datacite
-```
-
-### Pre-Deployment Check
-```bash
-# Check what would be updated before deployment
-node ace update:datacite --dry-run
-```
-
-### Debugging Sync Issues
-```bash
-# Investigate why specific dataset isn't syncing
-node ace update:datacite --stats --publish_id 231
-```
-
-### Full Resync
-```bash
-# Force update all DOI records (use with caution)
-node ace update:datacite --force
-```
-
-### Monitoring Report
-```bash
-# Generate sync status report
-node ace update:datacite --stats > datacite-sync-report.txt
-```
-
-## Best Practices
-
-1. **Regular Updates**: Run daily or after bulk dataset modifications
-2. **Test First**: Use `--dry-run` or `--stats` before bulk operations
-3. **Monitor Logs**: Check for data integrity warnings
-4. **Environment Separation**: Use correct API URLs for test vs production
-5. **Rate Limiting**: The command handles DataCite rate limits automatically
\ No newline at end of file
diff --git a/freshclam.conf b/freshclam.conf
index 31992be..ee82a23 100644
--- a/freshclam.conf
+++ b/freshclam.conf
@@ -1,47 +1,229 @@
##
-## Container-optimized freshclam configuration
+## Example config file for freshclam
+## Please read the freshclam.conf(5) manual before editing this file.
##
-# Database directory
+
+# Comment or remove the line below.
+
+# Path to the database directory.
+# WARNING: It must match clamd.conf's directive!
+# Default: hardcoded (depends on installation options)
DatabaseDirectory /var/lib/clamav
-# Log to stdout for container logging
+# Path to the log file (make sure it has proper permissions)
+# Default: disabled
# UpdateLogFile /dev/stdout
-# Basic logging settings
+# Maximum size of the log file.
+# Value of 0 disables the limit.
+# You may use 'M' or 'm' for megabytes (1M = 1m = 1048576 bytes)
+# and 'K' or 'k' for kilobytes (1K = 1k = 1024 bytes).
+# in bytes just don't use modifiers. If LogFileMaxSize is enabled,
+# log rotation (the LogRotate option) will always be enabled.
+# Default: 1M
+#LogFileMaxSize 2M
+
+# Log time with each message.
+# Default: no
LogTime yes
+
+# Enable verbose logging.
+# Default: no
LogVerbose yes
+
+# Use system logger (can work together with UpdateLogFile).
+# Default: no
LogSyslog no
-# PID file location
+# Specify the type of syslog messages - please refer to 'man syslog'
+# for facility names.
+# Default: LOG_LOCAL6
+#LogFacility LOG_MAIL
+
+# Enable log rotation. Always enabled when LogFileMaxSize is enabled.
+# Default: no
+#LogRotate yes
+
+# This option allows you to save the process identifier of the daemon
+# Default: disabled
+#PidFile /var/run/freshclam.pid
PidFile /var/run/clamav/freshclam.pid
-# Database owner
+# By default when started freshclam drops privileges and switches to the
+# "clamav" user. This directive allows you to change the database owner.
+# Default: clamav (may depend on installation options)
DatabaseOwner node
-# Mirror settings for Austria
+# Use DNS to verify virus database version. Freshclam uses DNS TXT records
+# to verify database and software versions. With this directive you can change
+# the database verification domain.
+# WARNING: Do not touch it unless you're configuring freshclam to use your
+# own database verification domain.
+# Default: current.cvd.clamav.net
+#DNSDatabaseInfo current.cvd.clamav.net
+
+# Uncomment the following line and replace XY with your country
+# code. See http://www.iana.org/cctld/cctld-whois.htm for the full list.
+# You can use db.XY.ipv6.clamav.net for IPv6 connections.
DatabaseMirror db.at.clamav.net
+
+# database.clamav.net is a round-robin record which points to our most
+# reliable mirrors. It's used as a fall back in case db.XY.clamav.net is
+# not working. DO NOT TOUCH the following line unless you know what you
+# are doing.
DatabaseMirror database.clamav.net
+# How many attempts to make before giving up.
+# Default: 3 (per mirror)
+#MaxAttempts 5
+
# With this option you can control scripted updates. It's highly recommended
# to keep it enabled.
# Default: yes
-# Update settings
-ScriptedUpdates yes
+#ScriptedUpdates yes
+
+# By default freshclam will keep the local databases (.cld) uncompressed to
+# make their handling faster. With this option you can enable the compression;
+# the change will take effect with the next database update.
+# Default: no
+#CompressLocalDatabase no
+
+# With this option you can provide custom sources (http:// or file://) for
+# database files. This option can be used multiple times.
+# Default: no custom URLs
+#DatabaseCustomURL http://myserver.com/mysigs.ndb
+#DatabaseCustomURL file:///mnt/nfs/local.hdb
+
+# This option allows you to easily point freshclam to private mirrors.
+# If PrivateMirror is set, freshclam does not attempt to use DNS
+# to determine whether its databases are out-of-date, instead it will
+# use the If-Modified-Since request or directly check the headers of the
+# remote database files. For each database, freshclam first attempts
+# to download the CLD file. If that fails, it tries to download the
+# CVD file. This option overrides DatabaseMirror, DNSDatabaseInfo
+# and ScriptedUpdates. It can be used multiple times to provide
+# fall-back mirrors.
+# Default: disabled
+#PrivateMirror mirror1.mynetwork.com
+#PrivateMirror mirror2.mynetwork.com
# Number of database checks per day.
# Default: 12 (every two hours)
-Checks 12
+#Checks 24
-# Don't fork (good for containers)
+# Proxy settings
+# Default: disabled
+#HTTPProxyServer myproxy.com
+#HTTPProxyPort 1234
+#HTTPProxyUsername myusername
+#HTTPProxyPassword mypass
+
+# If your servers are behind a firewall/proxy which applies User-Agent
+# filtering you can use this option to force the use of a different
+# User-Agent header.
+# Default: clamav/version_number
+#HTTPUserAgent SomeUserAgentIdString
+
+# Use aaa.bbb.ccc.ddd as client address for downloading databases. Useful for
+# multi-homed systems.
+# Default: Use OS'es default outgoing IP address.
+#LocalIPAddress aaa.bbb.ccc.ddd
+
+# Send the RELOAD command to clamd.
+# Default: no
+#NotifyClamd /path/to/clamd.conf
+
+# Run command after successful database update.
+# Default: disabled
+#OnUpdateExecute command
+
+# Run command when database update process fails.
+# Default: disabled
+#OnErrorExecute command
+
+# Run command when freshclam reports outdated version.
+# In the command string %v will be replaced by the new version number.
+# Default: disabled
+#OnOutdatedExecute command
+
+# Don't fork into background.
+# Default: no
Foreground no
-# Connection timeouts
-ConnectTimeout 60
-ReceiveTimeout 60
+# Enable debug messages in libclamav.
+# Default: no
+#Debug yes
-# Test databases before using them
-TestDatabases yes
+# Timeout in seconds when connecting to database server.
+# Default: 30
+#ConnectTimeout 60
-# Enable bytecode signatures
-Bytecode yes
\ No newline at end of file
+# Timeout in seconds when reading from database server.
+# Default: 30
+#ReceiveTimeout 60
+
+# With this option enabled, freshclam will attempt to load new
+# databases into memory to make sure they are properly handled
+# by libclamav before replacing the old ones.
+# Default: yes
+#TestDatabases yes
+
+# When enabled freshclam will submit statistics to the ClamAV Project about
+# the latest virus detections in your environment. The ClamAV maintainers
+# will then use this data to determine what types of malware are the most
+# detected in the field and in what geographic area they are.
+# Freshclam will connect to clamd in order to get recent statistics.
+# Default: no
+#SubmitDetectionStats /path/to/clamd.conf
+
+# Country of origin of malware/detection statistics (for statistical
+# purposes only). The statistics collector at ClamAV.net will look up
+# your IP address to determine the geographical origin of the malware
+# reported by your installation. If this installation is mainly used to
+# scan data which comes from a different location, please enable this
+# option and enter a two-letter code (see http://www.iana.org/domains/root/db/)
+# of the country of origin.
+# Default: disabled
+#DetectionStatsCountry country-code
+
+# This option enables support for our "Personal Statistics" service.
+# When this option is enabled, the information on malware detected by
+# your clamd installation is made available to you through our website.
+# To get your HostID, log on http://www.stats.clamav.net and add a new
+# host to your host list. Once you have the HostID, uncomment this option
+# and paste the HostID here. As soon as your freshclam starts submitting
+# information to our stats collecting service, you will be able to view
+# the statistics of this clamd installation by logging into
+# http://www.stats.clamav.net with the same credentials you used to
+# generate the HostID. For more information refer to:
+# http://www.clamav.net/documentation.html#cctts
+# This feature requires SubmitDetectionStats to be enabled.
+# Default: disabled
+#DetectionStatsHostID unique-id
+
+# This option enables support for Google Safe Browsing. When activated for
+# the first time, freshclam will download a new database file (safebrowsing.cvd)
+# which will be automatically loaded by clamd and clamscan during the next
+# reload, provided that the heuristic phishing detection is turned on. This
+# database includes information about websites that may be phishing sites or
+# possible sources of malware. When using this option, it's mandatory to run
+# freshclam at least every 30 minutes.
+# Freshclam uses the ClamAV's mirror infrastructure to distribute the
+# database and its updates but all the contents are provided under Google's
+# terms of use. See http://www.google.com/transparencyreport/safebrowsing
+# and http://www.clamav.net/documentation.html#safebrowsing
+# for more information.
+# Default: disabled
+#SafeBrowsing yes
+
+# This option enables downloading of bytecode.cvd, which includes additional
+# detection mechanisms and improvements to the ClamAV engine.
+# Default: enabled
+#Bytecode yes
+
+# Download an additional 3rd party signature database distributed through
+# the ClamAV mirrors.
+# This option can be used multiple times.
+#ExtraDatabase dbname1
+#ExtraDatabase dbname2
diff --git a/package-lock.json b/package-lock.json
index 7cb57a4..6b10877 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,7 +10,7 @@
"dependencies": {
"@adonisjs/auth": "^9.2.4",
"@adonisjs/bodyparser": "^10.0.1",
- "@adonisjs/core": "6.17.2",
+ "@adonisjs/core": "^6.17.0",
"@adonisjs/cors": "^2.2.1",
"@adonisjs/drive": "^3.2.0",
"@adonisjs/inertia": "^2.1.3",
@@ -30,6 +30,7 @@
"@phc/format": "^1.0.0",
"@poppinss/manager": "^5.0.2",
"@vinejs/vine": "^3.0.0",
+ "argon2": "^0.43.0",
"axios": "^1.7.9",
"bcrypt": "^5.1.1",
"bcryptjs": "^2.4.3",
@@ -108,9 +109,9 @@
}
},
"node_modules/@adonisjs/ace": {
- "version": "13.4.0",
- "resolved": "https://registry.npmjs.org/@adonisjs/ace/-/ace-13.4.0.tgz",
- "integrity": "sha512-7Wq6CpXmQm3m/6fKfzubAadCdiH2kKSni+K8s5KcTIFryKSqW+f06UAPOUwRJWqy80hnVlujAjveIsNJSPeJjA==",
+ "version": "13.3.0",
+ "resolved": "https://registry.npmjs.org/@adonisjs/ace/-/ace-13.3.0.tgz",
+ "integrity": "sha512-68dveDFd766p69cBvK/MtOrOP0+YKYLeHspa9KLEWcWk9suPf3pbGkHQ2pwDnvLJxBPHk4932KbbSSzzpGNZGw==",
"license": "MIT",
"dependencies": {
"@poppinss/cliui": "^6.4.1",
@@ -130,9 +131,9 @@
}
},
"node_modules/@adonisjs/application": {
- "version": "8.4.2",
- "resolved": "https://registry.npmjs.org/@adonisjs/application/-/application-8.4.2.tgz",
- "integrity": "sha512-gxyQgl1n7M/hv7ZKQOlTo2adBMehjEO0ssWSG3AGW2RXdCvkHQKlatFXMuXJMmGg2P1AWJX0LEiXey9+qxC9Uw==",
+ "version": "8.4.1",
+ "resolved": "https://registry.npmjs.org/@adonisjs/application/-/application-8.4.1.tgz",
+ "integrity": "sha512-2vwO/8DoKJ9AR4Vvllz08RcomBoETc3FMf+q+ri1BVVjc76tLGV3KcYZp8+uKOuEreiK6poQ7NwJrR1P5ANA/w==",
"license": "MIT",
"dependencies": {
"@poppinss/hooks": "^7.2.5",
@@ -181,13 +182,13 @@
}
},
"node_modules/@adonisjs/auth": {
- "version": "9.4.2",
- "resolved": "https://registry.npmjs.org/@adonisjs/auth/-/auth-9.4.2.tgz",
- "integrity": "sha512-Ifn838j9cQFxxin4bOURAiMrmwtu2g1NC5eYpw0p0QtD6hnnwOBqFiVWYcoYKquddiHKZ3x72mRd+x4MVIYzlQ==",
+ "version": "9.4.0",
+ "resolved": "https://registry.npmjs.org/@adonisjs/auth/-/auth-9.4.0.tgz",
+ "integrity": "sha512-dzvnJRKY+RcKUXCRT6ebnlGV0wAfejTSGqS0XbgjB97r6Pww14MhsY89EBr1nSydQzvjdbtIR3EDGbU97BVmbQ==",
"license": "MIT",
"dependencies": {
"@adonisjs/presets": "^2.6.4",
- "@poppinss/utils": "^6.10.0",
+ "@poppinss/utils": "^6.9.2",
"basic-auth": "^2.0.1"
},
"engines": {
@@ -257,30 +258,30 @@
}
},
"node_modules/@adonisjs/core": {
- "version": "6.17.2",
- "resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.17.2.tgz",
- "integrity": "sha512-POT5COID8Z3j37+Dd7Y1EfG01Q6+HPY/tGcSb0Y97W2VIPkFjqcW2ooTE4wFT09u7coNohtXJa19a0feMz9ncw==",
+ "version": "6.18.0",
+ "resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.18.0.tgz",
+ "integrity": "sha512-Uuj7kzlMPiS3MVOCHfiXLVeFXUqrjGjF43LNLJb4Q2hBY/q0T2kUym2kVO2gazkLWj8YQKLdOA4ij7t9rDR4OA==",
"license": "MIT",
"dependencies": {
"@adonisjs/ace": "^13.3.0",
- "@adonisjs/application": "^8.3.1",
- "@adonisjs/bodyparser": "^10.0.3",
+ "@adonisjs/application": "^8.4.1",
+ "@adonisjs/bodyparser": "^10.1.0",
"@adonisjs/config": "^5.0.2",
"@adonisjs/encryption": "^6.0.2",
- "@adonisjs/env": "^6.1.1",
+ "@adonisjs/env": "^6.2.0",
"@adonisjs/events": "^9.0.2",
"@adonisjs/fold": "^10.1.3",
- "@adonisjs/hash": "^9.0.5",
+ "@adonisjs/hash": "^9.1.1",
"@adonisjs/health": "^2.0.0",
- "@adonisjs/http-server": "^7.4.0",
- "@adonisjs/logger": "^6.0.5",
+ "@adonisjs/http-server": "^7.6.1",
+ "@adonisjs/logger": "^6.0.6",
"@adonisjs/repl": "^4.1.0",
- "@antfu/install-pkg": "^1.0.0",
+ "@antfu/install-pkg": "^1.1.0",
"@paralleldrive/cuid2": "^2.2.2",
"@poppinss/colors": "^4.1.4",
- "@poppinss/dumper": "^0.6.2",
+ "@poppinss/dumper": "^0.6.3",
"@poppinss/macroable": "^1.0.4",
- "@poppinss/utils": "^6.9.2",
+ "@poppinss/utils": "^6.9.3",
"@sindresorhus/is": "^7.0.1",
"@types/he": "^1.2.3",
"error-stack-parser-es": "^1.0.5",
@@ -300,8 +301,8 @@
"peerDependencies": {
"@adonisjs/assembler": "^7.8.0",
"@vinejs/vine": "^2.1.0 || ^3.0.0",
- "argon2": "^0.31.2 || ^0.41.0",
- "bcrypt": "^5.1.1",
+ "argon2": "^0.31.2 || ^0.41.0 || ^0.43.0",
+ "bcrypt": "^5.1.1 || ^6.0.0",
"edge.js": "^6.2.0"
},
"peerDependenciesMeta": {
@@ -446,49 +447,17 @@
}
},
"node_modules/@adonisjs/fold": {
- "version": "10.2.0",
- "resolved": "https://registry.npmjs.org/@adonisjs/fold/-/fold-10.2.0.tgz",
- "integrity": "sha512-VDBGrVz2viaCsmONLKYpMMeP3ds+fw+7kofeF/z9ic6cB3d7BLEB8VcIdGkfY0FCBbLK2Btee1tNPuUF1uMlmQ==",
+ "version": "10.1.3",
+ "resolved": "https://registry.npmjs.org/@adonisjs/fold/-/fold-10.1.3.tgz",
+ "integrity": "sha512-wzeuWMXx9SoJkNO4ycoyfxzoSyyMy3umVxb9cbzeWR/sYNVgi50l+vgJc634+lxpCE0RFTpxCv1M235EWDF9SQ==",
"license": "MIT",
"dependencies": {
- "@poppinss/utils": "^7.0.0-next.1",
- "parse-imports": "^2.2.1"
+ "@poppinss/utils": "^6.8.3"
},
"engines": {
"node": ">=18.16.0"
}
},
- "node_modules/@adonisjs/fold/node_modules/@poppinss/utils": {
- "version": "7.0.0-next.3",
- "resolved": "https://registry.npmjs.org/@poppinss/utils/-/utils-7.0.0-next.3.tgz",
- "integrity": "sha512-Z+3kolI/gdjTQRJWRiZTEk6r6QOeGLesfmdc8ISSeHlyUg0mTnVdi08/rwOcRJD6dLdwBGTDUf7lK2K7GpT4ww==",
- "license": "MIT",
- "dependencies": {
- "@poppinss/exception": "^1.2.1",
- "@poppinss/object-builder": "^1.1.0",
- "@poppinss/string": "^1.6.0",
- "@poppinss/types": "^1.1.0",
- "flattie": "^1.1.1",
- "safe-stable-stringify": "^2.5.0",
- "secure-json-parse": "^4.0.0"
- }
- },
- "node_modules/@adonisjs/fold/node_modules/secure-json-parse": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/secure-json-parse/-/secure-json-parse-4.0.0.tgz",
- "integrity": "sha512-dxtLJO6sc35jWidmLxo7ij+Eg48PM/kleBsxpC8QJE0qJICe+KawkDQmvCMZUr9u7WKVHgMW6vy3fQ7zMiFZMA==",
- "funding": [
- {
- "type": "github",
- "url": "https://github.com/sponsors/fastify"
- },
- {
- "type": "opencollective",
- "url": "https://opencollective.com/fastify"
- }
- ],
- "license": "BSD-3-Clause"
- },
"node_modules/@adonisjs/hash": {
"version": "9.1.1",
"resolved": "https://registry.npmjs.org/@adonisjs/hash/-/hash-9.1.1.tgz",
@@ -528,17 +497,17 @@
}
},
"node_modules/@adonisjs/http-server": {
- "version": "7.7.0",
- "resolved": "https://registry.npmjs.org/@adonisjs/http-server/-/http-server-7.7.0.tgz",
- "integrity": "sha512-qW1wsp7f1BqRO2qmJ8laUaq8vnLjEvhgkMusLEa2ju6RBMMsph5w3cEDTXAwQO8fSSqNXmRTzPRQ1lUm/FXq0A==",
+ "version": "7.6.1",
+ "resolved": "https://registry.npmjs.org/@adonisjs/http-server/-/http-server-7.6.1.tgz",
+ "integrity": "sha512-2KHen5rcer6pDvJrDOhr5hJ9cSxSOOrdqmm9o9HkW/BAkMh42ymTIvCtaMmz6amrCSg0cdMO3ImmD8VBaMmfXA==",
"license": "MIT",
"dependencies": {
"@paralleldrive/cuid2": "^2.2.2",
"@poppinss/macroable": "^1.0.4",
"@poppinss/matchit": "^3.1.2",
"@poppinss/middleware": "^3.2.5",
- "@poppinss/utils": "^6.10.0",
- "@sindresorhus/is": "^7.0.2",
+ "@poppinss/utils": "^6.9.3",
+ "@sindresorhus/is": "^7.0.1",
"accepts": "^1.3.8",
"content-disposition": "^0.5.4",
"cookie": "^1.0.2",
@@ -611,16 +580,16 @@
}
},
"node_modules/@adonisjs/lucid": {
- "version": "21.8.0",
- "resolved": "https://registry.npmjs.org/@adonisjs/lucid/-/lucid-21.8.0.tgz",
- "integrity": "sha512-AgS3l/J70q0K1ZTAbNVQTZuQWvCDwnj6a2rXCFu/aYRtIdbnGPLV0kIQ76WbdtlstUnKj8GFY/JNwok1TuTVVg==",
+ "version": "21.6.1",
+ "resolved": "https://registry.npmjs.org/@adonisjs/lucid/-/lucid-21.6.1.tgz",
+ "integrity": "sha512-0TLCcPm9GHShJlsDAF5SHilafnvTxW25y5nD3bGJBSMEaNfGXcGRBbnyWoeNs7DsnqMCZ6ociT+0XMcKJWzQrQ==",
"license": "MIT",
"dependencies": {
"@adonisjs/presets": "^2.6.4",
- "@faker-js/faker": "^9.9.0",
- "@poppinss/hooks": "^7.2.6",
- "@poppinss/macroable": "^1.0.5",
- "@poppinss/utils": "^6.10.0",
+ "@faker-js/faker": "^9.6.0",
+ "@poppinss/hooks": "^7.2.5",
+ "@poppinss/macroable": "^1.0.4",
+ "@poppinss/utils": "^6.9.2",
"fast-deep-equal": "^3.1.3",
"igniculus": "^1.5.0",
"kleur": "^4.1.5",
@@ -718,12 +687,12 @@
}
},
"node_modules/@adonisjs/repl": {
- "version": "4.1.2",
- "resolved": "https://registry.npmjs.org/@adonisjs/repl/-/repl-4.1.2.tgz",
- "integrity": "sha512-NnczRJusl0082GOjEFYwObW/yBGJtpfJFnkFCQdQ6eykgBHVNYaY6qstfob+l1bedetRj0hrDY6YfsWMkA0MCg==",
+ "version": "4.1.0",
+ "resolved": "https://registry.npmjs.org/@adonisjs/repl/-/repl-4.1.0.tgz",
+ "integrity": "sha512-7Ml87uoufDQmpjRZYbJeRTk0/WcD4DllJ96L1r2IWF/jZIsryiVN5o+7Xd7fHlRzd8iapAbs32Tq4a6fVI6UKA==",
"license": "MIT",
"dependencies": {
- "@poppinss/colors": "^4.1.5",
+ "@poppinss/colors": "^4.1.4",
"string-width": "^7.2.0"
},
"engines": {
@@ -868,6 +837,21 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
+ "node_modules/@ampproject/remapping": {
+ "version": "2.3.0",
+ "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz",
+ "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==",
+ "dev": true,
+ "license": "Apache-2.0",
+ "peer": true,
+ "dependencies": {
+ "@jridgewell/gen-mapping": "^0.3.5",
+ "@jridgewell/trace-mapping": "^0.3.24"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
"node_modules/@antfu/install-pkg": {
"version": "0.4.1",
"resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.4.1.tgz",
@@ -891,641 +875,6 @@
"node": ">=4"
}
},
- "node_modules/@aws-crypto/sha256-browser": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-5.2.0.tgz",
- "integrity": "sha512-AXfN/lGotSQwu6HNcEsIASo7kWXZ5HYWvfOmSNKDsEqC4OashTp8alTmaz+F7TC2L083SFv5RdB+qU3Vs1kZqw==",
- "license": "Apache-2.0",
- "dependencies": {
- "@aws-crypto/sha256-js": "^5.2.0",
- "@aws-crypto/supports-web-crypto": "^5.2.0",
- "@aws-crypto/util": "^5.2.0",
- "@aws-sdk/types": "^3.222.0",
- "@aws-sdk/util-locate-window": "^3.0.0",
- "@smithy/util-utf8": "^2.0.0",
- "tslib": "^2.6.2"
- }
- },
- "node_modules/@aws-crypto/sha256-browser/node_modules/@smithy/is-array-buffer": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/@smithy/is-array-buffer/-/is-array-buffer-2.2.0.tgz",
- "integrity": "sha512-GGP3O9QFD24uGeAXYUjwSTXARoqpZykHadOmA8G5vfJPK0/DC67qa//0qvqrJzL1xc8WQWX7/yc7fwudjPHPhA==",
- "license": "Apache-2.0",
- "dependencies": {
- "tslib": "^2.6.2"
- },
- "engines": {
- "node": ">=14.0.0"
- }
- },
- "node_modules/@aws-crypto/sha256-browser/node_modules/@smithy/util-buffer-from": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/@smithy/util-buffer-from/-/util-buffer-from-2.2.0.tgz",
- "integrity": "sha512-IJdWBbTcMQ6DA0gdNhh/BwrLkDR+ADW5Kr1aZmd4k3DIF6ezMV4R2NIAmT08wQJ3yUK82thHWmC/TnK/wpMMIA==",
- "license": "Apache-2.0",
- "dependencies": {
- "@smithy/is-array-buffer": "^2.2.0",
- "tslib": "^2.6.2"
- },
- "engines": {
- "node": ">=14.0.0"
- }
- },
- "node_modules/@aws-crypto/sha256-browser/node_modules/@smithy/util-utf8": {
- "version": "2.3.0",
- "resolved": "https://registry.npmjs.org/@smithy/util-utf8/-/util-utf8-2.3.0.tgz",
- "integrity": "sha512-R8Rdn8Hy72KKcebgLiv8jQcQkXoLMOGGv5uI1/k0l+snqkOzQ1R0ChUBCxWMlBsFMekWjq0wRudIweFs7sKT5A==",
- "license": "Apache-2.0",
- "dependencies": {
- "@smithy/util-buffer-from": "^2.2.0",
- "tslib": "^2.6.2"
- },
- "engines": {
- "node": ">=14.0.0"
- }
- },
- "node_modules/@aws-crypto/sha256-js": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-js/-/sha256-js-5.2.0.tgz",
- "integrity": "sha512-FFQQyu7edu4ufvIZ+OadFpHHOt+eSTBaYaki44c+akjg7qZg9oOQeLlk77F6tSYqjDAFClrHJk9tMf0HdVyOvA==",
- "license": "Apache-2.0",
- "dependencies": {
- "@aws-crypto/util": "^5.2.0",
- "@aws-sdk/types": "^3.222.0",
- "tslib": "^2.6.2"
- },
- "engines": {
- "node": ">=16.0.0"
- }
- },
- "node_modules/@aws-crypto/supports-web-crypto": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/@aws-crypto/supports-web-crypto/-/supports-web-crypto-5.2.0.tgz",
- "integrity": "sha512-iAvUotm021kM33eCdNfwIN//F77/IADDSs58i+MDaOqFrVjZo9bAal0NK7HurRuWLLpF1iLX7gbWrjHjeo+YFg==",
- "license": "Apache-2.0",
- "dependencies": {
- "tslib": "^2.6.2"
- }
- },
- "node_modules/@aws-crypto/util": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/@aws-crypto/util/-/util-5.2.0.tgz",
- "integrity": "sha512-4RkU9EsI6ZpBve5fseQlGNUWKMa1RLPQ1dnjnQoe07ldfIzcsGb5hC5W0Dm7u423KWzawlrpbjXBrXCEv9zazQ==",
- "license": "Apache-2.0",
- "dependencies": {
- "@aws-sdk/types": "^3.222.0",
- "@smithy/util-utf8": "^2.0.0",
- "tslib": "^2.6.2"
- }
- },
- "node_modules/@aws-crypto/util/node_modules/@smithy/is-array-buffer": {
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+ "resolved": "https://registry.npmjs.org/@jsonjoy.com/util/-/util-1.6.0.tgz",
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"license": "Apache-2.0",
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- "@jsonjoy.com/codegen": "^1.0.0"
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- "resolved": "https://registry.npmjs.org/@pkgr/core/-/core-0.2.9.tgz",
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+ "resolved": "https://registry.npmjs.org/@poppinss/cliui/-/cliui-6.4.3.tgz",
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+ "@poppinss/colors": "^4.1.4",
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@@ -3341,39 +2602,51 @@
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"terminal-size": "^4.0.0",
"wordwrap": "^1.0.0"
+ },
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}
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- "resolved": "https://registry.npmjs.org/@poppinss/colors/-/colors-4.1.5.tgz",
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+ "version": "4.1.4",
+ "resolved": "https://registry.npmjs.org/@poppinss/colors/-/colors-4.1.4.tgz",
+ "integrity": "sha512-FA+nTU8p6OcSH4tLDY5JilGYr1bVWHpNmcLr7xmMEdbWmKHa+3QZ+DqefrXKmdjO/brHTnQZo20lLSjaO7ydog==",
"license": "MIT",
"dependencies": {
"kleur": "^4.1.5"
+ },
+ "engines": {
+ "node": ">=18.16.0"
}
},
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- "resolved": "https://registry.npmjs.org/@poppinss/dumper/-/dumper-0.6.4.tgz",
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+ "version": "0.6.3",
+ "resolved": "https://registry.npmjs.org/@poppinss/dumper/-/dumper-0.6.3.tgz",
+ "integrity": "sha512-iombbn8ckOixMtuV1p3f8jN6vqhXefNjJttoPaJDMeIk/yIGhkkL3OrHkEjE9SRsgoAx1vBUU2GtgggjvA5hCA==",
"license": "MIT",
"dependencies": {
- "@poppinss/colors": "^4.1.5",
- "@sindresorhus/is": "^7.0.2",
+ "@poppinss/colors": "^4.1.4",
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}
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- "license": "MIT"
+ "version": "1.2.1",
+ "resolved": "https://registry.npmjs.org/@poppinss/exception/-/exception-1.2.1.tgz",
+ "integrity": "sha512-aQypoot0HPSJa6gDPEPTntc1GT6QINrSbgRlRhadGW2WaYqUK3tK4Bw9SBMZXhmxd3GeAlZjVcODHgiu+THY7A==",
+ "license": "MIT",
+ "engines": {
+ "node": ">=18"
+ }
},
"node_modules/@poppinss/hooks": {
- "version": "7.2.6",
- "resolved": "https://registry.npmjs.org/@poppinss/hooks/-/hooks-7.2.6.tgz",
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+ "version": "7.2.5",
+ "resolved": "https://registry.npmjs.org/@poppinss/hooks/-/hooks-7.2.5.tgz",
+ "integrity": "sha512-mxORKQ5CFzQNi6yK3zwCGWfGS507w23IhV3kFq42QzWlv/vpvf4aMJDbtfMCR5p52ghVoe0d1wmgp77ak2ORhQ==",
+ "license": "MIT",
+ "engines": {
+ "node": ">=18.16.0"
+ }
},
"node_modules/@poppinss/inspect": {
"version": "1.0.1",
@@ -3385,10 +2658,13 @@
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- "license": "MIT"
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/@poppinss/macroable/-/macroable-1.0.4.tgz",
+ "integrity": "sha512-ct43jurbe7lsUX5eIrj4ijO3j/6zIPp7CDnFWXDs7UPAbw1Pu1iH3oAmFdP4jcskKJBURH5M9oTtyeiUXyHX8Q==",
+ "license": "MIT",
+ "engines": {
+ "node": ">=18.16.0"
+ }
},
"node_modules/@poppinss/manager": {
"version": "5.0.2",
@@ -3397,19 +2673,22 @@
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+ "resolved": "https://registry.npmjs.org/@poppinss/matchit/-/matchit-3.1.2.tgz",
+ "integrity": "sha512-Bx+jY+vmdQFmwYiHliiPjr+oVBaGnh79B1h1FSAm3jME1QylLFt8PPYC0ymO8Q5PzJj/KuE3jeTnZhRHOWqq8g==",
"license": "MIT",
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}
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- "license": "MIT"
+ "version": "3.2.5",
+ "resolved": "https://registry.npmjs.org/@poppinss/middleware/-/middleware-3.2.5.tgz",
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+ "license": "MIT",
+ "engines": {
+ "node": ">=18.16.0"
+ }
},
"node_modules/@poppinss/multiparty": {
"version": "2.0.1",
@@ -3432,21 +2711,24 @@
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+ "version": "3.1.4",
+ "resolved": "https://registry.npmjs.org/@poppinss/prompts/-/prompts-3.1.4.tgz",
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"license": "MIT",
"dependencies": {
- "@poppinss/colors": "^4.1.5",
- "@poppinss/exception": "^1.2.1",
+ "@poppinss/colors": "^4.1.4",
+ "@poppinss/exception": "^1.1.0",
"@poppinss/object-builder": "^1.1.0",
"enquirer": "^2.4.1"
+ },
+ "engines": {
+ "node": ">=18.16.0"
}
},
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- "version": "1.7.0",
- "resolved": "https://registry.npmjs.org/@poppinss/string/-/string-1.7.0.tgz",
- "integrity": "sha512-IuCtWaUwmJeAdby0n1a5cTYsBLe7fPymdc4oNTTl1b6l+Ok+14XpSX0ILOEU6UtZ9D2XI3f4TVUh4Titkk1xgw==",
+ "version": "1.6.0",
+ "resolved": "https://registry.npmjs.org/@poppinss/string/-/string-1.6.0.tgz",
+ "integrity": "sha512-HfAf9VqTvo31BsruwgwEauQ316RNODdryk6QgYZo4qTV50s0h1H9HmIr+QjwwI3u4Sz7r4Q1dd1EVaLB7pWlaw==",
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@@ -3459,16 +2741,10 @@
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+ "resolved": "https://registry.npmjs.org/@poppinss/utils/-/utils-6.9.4.tgz",
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@@ -3499,27 +2775,27 @@
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+ "resolved": "https://registry.npmjs.org/@poppinss/validator-lite/-/validator-lite-2.1.0.tgz",
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+ "resolved": "https://registry.npmjs.org/@redis/bloom/-/bloom-5.5.5.tgz",
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"license": "MIT",
"engines": {
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+ "resolved": "https://registry.npmjs.org/@redis/client/-/client-5.5.5.tgz",
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@@ -3529,45 +2805,45 @@
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"license": "MIT",
"engines": {
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},
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+ "@redis/client": "^5.5.5"
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+ "resolved": "https://registry.npmjs.org/@redis/search/-/search-5.5.5.tgz",
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},
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+ "resolved": "https://registry.npmjs.org/@redis/time-series/-/time-series-5.5.5.tgz",
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"license": "MIT",
"engines": {
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},
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+ "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.41.1.tgz",
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- "integrity": "sha512-7b0dTKR3Ed//AD/6kkx/o7duS8H3f1a4w3BYpIriX4BzIhjkn4teo05cptsxvLesHFKK5KObnadmCHBwGc+51A==",
+ "version": "5.99.9",
+ "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.99.9.tgz",
+ "integrity": "sha512-brOPwM3JnmOa+7kd3NsmOUOwbDAj8FT9xDsG3IW0MgbN9yZV7Oi/s/+MNQ/EcSMqw7qfoRyXPoeEWT8zLVdVGg==",
"dev": true,
"license": "MIT",
"peer": true,
"dependencies": {
"@types/eslint-scope": "^3.7.7",
- "@types/estree": "^1.0.8",
+ "@types/estree": "^1.0.6",
"@types/json-schema": "^7.0.15",
"@webassemblyjs/ast": "^1.14.1",
"@webassemblyjs/wasm-edit": "^1.14.1",
"@webassemblyjs/wasm-parser": "^1.14.1",
- "acorn": "^8.15.0",
- "acorn-import-phases": "^1.0.3",
+ "acorn": "^8.14.0",
"browserslist": "^4.24.0",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^5.17.3",
+ "enhanced-resolve": "^5.17.1",
"es-module-lexer": "^1.2.1",
"eslint-scope": "5.1.1",
"events": "^3.2.0",
@@ -15421,7 +13969,7 @@
"tapable": "^2.1.1",
"terser-webpack-plugin": "^5.3.11",
"watchpack": "^2.4.1",
- "webpack-sources": "^3.3.3"
+ "webpack-sources": "^3.2.3"
},
"bin": {
"webpack": "bin/webpack.js"
@@ -15440,15 +13988,15 @@
}
},
"node_modules/webpack-dev-middleware": {
- "version": "7.4.3",
- "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-7.4.3.tgz",
- "integrity": "sha512-5kA/PzpZzDz5mNOkcNLmU1UdjGeSSxd7rt1akWpI70jMNHLASiBPRaQZn0hgyhvhawfIwSnnLfDABIxL3ueyFg==",
+ "version": "7.4.2",
+ "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-7.4.2.tgz",
+ "integrity": "sha512-xOO8n6eggxnwYpy1NlzUKpvrjfJTvae5/D6WOK0S2LSo7vjmo5gCM1DbLUmFqrMTJP+W/0YZNctm7jasWvLuBA==",
"dev": true,
"license": "MIT",
"dependencies": {
"colorette": "^2.0.10",
"memfs": "^4.6.0",
- "mime-types": "^3.0.1",
+ "mime-types": "^2.1.31",
"on-finished": "^2.4.1",
"range-parser": "^1.2.1",
"schema-utils": "^4.0.0"
@@ -15469,6 +14017,29 @@
}
}
},
+ "node_modules/webpack-dev-middleware/node_modules/mime-db": {
+ "version": "1.52.0",
+ "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.52.0.tgz",
+ "integrity": "sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": ">= 0.6"
+ }
+ },
+ "node_modules/webpack-dev-middleware/node_modules/mime-types": {
+ "version": "2.1.35",
+ "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.35.tgz",
+ "integrity": "sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw==",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "mime-db": "1.52.0"
+ },
+ "engines": {
+ "node": ">= 0.6"
+ }
+ },
"node_modules/webpack-dev-server": {
"version": "5.2.2",
"resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.2.tgz",
@@ -15602,9 +14173,9 @@
}
},
"node_modules/webpack-sources": {
- "version": "3.3.3",
- "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.3.3.tgz",
- "integrity": "sha512-yd1RBzSGanHkitROoPFd6qsrxt+oFhg/129YzheDGqeustzX0vTZJZsSsQjVQC4yzBQ56K55XU8gaNCtIzOnTg==",
+ "version": "3.3.2",
+ "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.3.2.tgz",
+ "integrity": "sha512-ykKKus8lqlgXX/1WjudpIEjqsafjOTcOJqxnAbMLAu/KCsDCJ6GBtvscewvTkrn24HsnvFwrSCbenFrhtcCsAA==",
"dev": true,
"license": "MIT",
"peer": true,
@@ -15775,9 +14346,9 @@
"license": "MIT"
},
"node_modules/wrap-ansi": {
- "version": "9.0.2",
- "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.2.tgz",
- "integrity": "sha512-42AtmgqjV+X1VpdOfyTGOYRi0/zsoLqtXQckTmqTeybT+BDIbM/Guxo7x3pE2vtpr1ok6xRqM9OpBe+Jyoqyww==",
+ "version": "9.0.0",
+ "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz",
+ "integrity": "sha512-G8ura3S+3Z2G+mkgNRq8dqaFZAuxfsxpBB8OCTGRTCtp+l/v9nbFNmCUP1BZMts3G1142MsZfn6eeUKrr4PD1Q==",
"license": "MIT",
"dependencies": {
"ansi-styles": "^6.2.1",
@@ -15843,9 +14414,9 @@
}
},
"node_modules/wrap-ansi/node_modules/ansi-regex": {
- "version": "6.2.2",
- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz",
- "integrity": "sha512-Bq3SmSpyFHaWjPk8If9yc6svM8c56dB5BAtW4Qbw5jHTwwXXcTLoRMkpDJp6VL0XzlWaCHTXrkFURMYmD0sLqg==",
+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz",
+ "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==",
"license": "MIT",
"engines": {
"node": ">=12"
@@ -15855,9 +14426,9 @@
}
},
"node_modules/wrap-ansi/node_modules/ansi-styles": {
- "version": "6.2.3",
- "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.3.tgz",
- "integrity": "sha512-4Dj6M28JB+oAH8kFkTLUo+a2jwOFkuqb3yucU0CANcRRUbxS0cP0nZYCGjcc3BNXwRIsUVmDGgzawme7zvJHvg==",
+ "version": "6.2.1",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.1.tgz",
+ "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug==",
"license": "MIT",
"engines": {
"node": ">=12"
@@ -15867,9 +14438,9 @@
}
},
"node_modules/wrap-ansi/node_modules/strip-ansi": {
- "version": "7.1.2",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.2.tgz",
- "integrity": "sha512-gmBGslpoQJtgnMAvOVqGZpEz9dyoKTCzy2nfz/n8aIFhN/jCE/rCmcxabB6jOOHV+0WNnylOxaxBQPSvcWklhA==",
+ "version": "7.1.0",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz",
+ "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==",
"license": "MIT",
"dependencies": {
"ansi-regex": "^6.0.1"
@@ -15888,9 +14459,9 @@
"license": "ISC"
},
"node_modules/ws": {
- "version": "8.18.3",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.3.tgz",
- "integrity": "sha512-PEIGCY5tSlUt50cqyMXfCzX+oOPqN0vuGqWzbcJ2xvnkzkq46oOpz7dQaTDBdfICb4N14+GARUDw2XV2N4tvzg==",
+ "version": "8.18.2",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.2.tgz",
+ "integrity": "sha512-DMricUmwGZUVr++AEAe2uiVM7UoO9MAVZMDu05UQOaUII0lp+zOzLLU4Xqh/JvTqklB1T4uELaaPBKyjE1r4fQ==",
"dev": true,
"license": "MIT",
"engines": {
@@ -15909,22 +14480,6 @@
}
}
},
- "node_modules/wsl-utils": {
- "version": "0.1.0",
- "resolved": "https://registry.npmjs.org/wsl-utils/-/wsl-utils-0.1.0.tgz",
- "integrity": "sha512-h3Fbisa2nKGPxCpm89Hk33lBLsnaGBvctQopaBSOW/uIs6FTe1ATyAnKFJrzVs9vpGdsTe73WF3V4lIsk4Gacw==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "is-wsl": "^3.1.0"
- },
- "engines": {
- "node": ">=18"
- },
- "funding": {
- "url": "https://github.com/sponsors/sindresorhus"
- }
- },
"node_modules/xmlbuilder2": {
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/xmlbuilder2/-/xmlbuilder2-3.1.1.tgz",
@@ -16000,9 +14555,9 @@
"peer": true
},
"node_modules/yaml": {
- "version": "2.8.1",
- "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.1.tgz",
- "integrity": "sha512-lcYcMxX2PO9XMGvAJkJ3OsNMw+/7FKes7/hgerGUYWIoWu5j/+YQqcZr5JnPZWzOsEBgMbSbiSTn/dv/69Mkpw==",
+ "version": "2.8.0",
+ "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.0.tgz",
+ "integrity": "sha512-4lLa/EcQCB0cJkyts+FpIRx5G/llPxfP6VQU5KByHEhLxY3IJCH0f0Hy1MHI8sClTvsIb8qwRJ6R/ZdlDJ/leQ==",
"devOptional": true,
"license": "ISC",
"bin": {
@@ -16169,9 +14724,9 @@
}
},
"node_modules/yoctocolors": {
- "version": "2.1.2",
- "resolved": "https://registry.npmjs.org/yoctocolors/-/yoctocolors-2.1.2.tgz",
- "integrity": "sha512-CzhO+pFNo8ajLM2d2IW/R93ipy99LWjtwblvC1RsoSUMZgyLbYFr221TnSNT7GjGdYui6P459mw9JH/g/zW2ug==",
+ "version": "2.1.1",
+ "resolved": "https://registry.npmjs.org/yoctocolors/-/yoctocolors-2.1.1.tgz",
+ "integrity": "sha512-GQHQqAopRhwU8Kt1DDM8NjibDXHC8eoh1erhGAJPEyveY9qqVeXvVikNKrDz69sHowPMorbPUrH/mx8c50eiBQ==",
"devOptional": true,
"license": "MIT",
"engines": {
@@ -16193,14 +14748,17 @@
}
},
"node_modules/youch-core": {
- "version": "0.3.3",
- "resolved": "https://registry.npmjs.org/youch-core/-/youch-core-0.3.3.tgz",
- "integrity": "sha512-ho7XuGjLaJ2hWHoK8yFnsUGy2Y5uDpqSTq1FkHLK4/oqKtyUU1AFbOOxY4IpC9f0fTLjwYbslUz0Po5BpD1wrA==",
+ "version": "0.3.2",
+ "resolved": "https://registry.npmjs.org/youch-core/-/youch-core-0.3.2.tgz",
+ "integrity": "sha512-fusrlIMLeRvTFYLUjJ9KzlGC3N+6MOPJ68HNj/yJv2nz7zq8t4HEviLms2gkdRPUS7F5rZ5n+pYx9r88m6IE1g==",
"devOptional": true,
"license": "MIT",
"dependencies": {
- "@poppinss/exception": "^1.2.2",
+ "@poppinss/exception": "^1.2.0",
"error-stack-parser-es": "^1.0.5"
+ },
+ "engines": {
+ "node": ">=18"
}
},
"node_modules/youch-terminal": {
diff --git a/package.json b/package.json
index 7ae829f..989a29e 100644
--- a/package.json
+++ b/package.json
@@ -77,7 +77,7 @@
"dependencies": {
"@adonisjs/auth": "^9.2.4",
"@adonisjs/bodyparser": "^10.0.1",
- "@adonisjs/core": "6.17.2",
+ "@adonisjs/core": "^6.17.0",
"@adonisjs/cors": "^2.2.1",
"@adonisjs/drive": "^3.2.0",
"@adonisjs/inertia": "^2.1.3",
@@ -97,6 +97,7 @@
"@phc/format": "^1.0.0",
"@poppinss/manager": "^5.0.2",
"@vinejs/vine": "^3.0.0",
+ "argon2": "^0.43.0",
"axios": "^1.7.9",
"bcrypt": "^5.1.1",
"bcryptjs": "^2.4.3",
diff --git a/providers/rule_provider.ts b/providers/rule_provider.ts
deleted file mode 100644
index c945a5d..0000000
--- a/providers/rule_provider.ts
+++ /dev/null
@@ -1,34 +0,0 @@
-import { ApplicationService } from '@adonisjs/core/types';
-
-export default class RuleProvider {
- constructor(protected app: ApplicationService) {}
-
- public register() {
- // Register your own bindings
- }
-
- public async boot() {
- // IoC container is ready
- // await import("../src/rules/index.js");
-
- await import('#start/rules/unique');
- await import('#start/rules/translated_language');
- await import('#start/rules/unique_person');
- // () => import('#start/rules/file_length'),
- // () => import('#start/rules/file_scan'),
- // () => import('#start/rules/allowed_extensions_mimetypes'),
- await import('#start/rules/dependent_array_min_length');
- await import('#start/rules/referenceValidation');
- await import('#start/rules/valid_mimetype');
- await import('#start/rules/array_contains_types');
- await import('#start/rules/orcid');
- }
-
- public async ready() {
- // App is ready
- }
-
- public async shutdown() {
- // Cleanup, since app is going down
- }
-}
diff --git a/providers/vinejs_provider.ts b/providers/vinejs_provider.ts
index 568dd3e..e4aad4c 100644
--- a/providers/vinejs_provider.ts
+++ b/providers/vinejs_provider.ts
@@ -6,16 +6,17 @@
import type { ApplicationService } from '@adonisjs/core/types';
import vine, { symbols, BaseLiteralType, Vine } from '@vinejs/vine';
import type { FieldContext, FieldOptions } from '@vinejs/vine/types';
+// import type { MultipartFile, FileValidationOptions } from '@adonisjs/bodyparser/types';
import type { MultipartFile } from '@adonisjs/core/bodyparser';
import type { FileValidationOptions } from '@adonisjs/core/types/bodyparser';
import { Request, RequestValidator } from '@adonisjs/core/http';
import MimeType from '#models/mime_type';
+
/**
* Validation options accepted by the "file" rule
*/
export type FileRuleValidationOptions = Partial | ((field: FieldContext) => Partial);
-
/**
* Extend VineJS
*/
@@ -24,7 +25,6 @@ declare module '@vinejs/vine' {
myfile(options?: FileRuleValidationOptions): VineMultipartFile;
}
}
-
/**
* Extend HTTP request class
*/
@@ -36,54 +36,19 @@ declare module '@adonisjs/core/http' {
* Checks if the value is an instance of multipart file
* from bodyparser.
*/
-export function isBodyParserFile(file: MultipartFile | unknown): file is MultipartFile {
+export function isBodyParserFile(file: MultipartFile | unknown): boolean {
return !!(file && typeof file === 'object' && 'isMultipartFile' in file);
}
+export async function getEnabledExtensions() {
+ const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec();
+ const extensions = enabledExtensions
+ .map((extension) => {
+ return extension.file_extension.split('|');
+ })
+ .flat();
-/**
- * Cache for enabled extensions to reduce database queries
- */
-let extensionsCache: string[] | null = null;
-let cacheTimestamp = 0;
-const CACHE_DURATION = 5 * 60 * 1000; // 5 minutes
-
-/**
- * Get enabled extensions with caching
- */
-export async function getEnabledExtensions(): Promise {
- const now = Date.now();
-
- if (extensionsCache && now - cacheTimestamp < CACHE_DURATION) {
- return extensionsCache;
- }
-
- try {
- const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec();
-
- const extensions = enabledExtensions
- .map((extension) => extension.file_extension.split('|'))
- .flat()
- .map((ext) => ext.toLowerCase().trim())
- .filter((ext) => ext.length > 0);
-
- extensionsCache = [...new Set(extensions)]; // Remove duplicates
- cacheTimestamp = now;
-
- return extensionsCache;
- } catch (error) {
- console.error('Error fetching enabled extensions:', error);
- return extensionsCache || [];
- }
+ return extensions;
}
-
-/**
- * Clear extensions cache
- */
-export function clearExtensionsCache(): void {
- extensionsCache = null;
- cacheTimestamp = 0;
-}
-
/**
* VineJS validation rule that validates the file to be an
* instance of BodyParser MultipartFile class.
@@ -100,7 +65,6 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op
// At this point, you can use type assertion to explicitly tell TypeScript that file is of type MultipartFile
const validatedFile = file as MultipartFile;
const validationOptions = typeof options === 'function' ? options(field) : options;
-
/**
* Set size when it's defined in the options and missing
* on the file instance
@@ -108,29 +72,30 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op
if (validatedFile.sizeLimit === undefined && validationOptions.size) {
validatedFile.sizeLimit = validationOptions.size;
}
-
/**
* Set extensions when it's defined in the options and missing
* on the file instance
*/
- if (validatedFile.allowedExtensions === undefined) {
- if (validationOptions.extnames !== undefined) {
- validatedFile.allowedExtensions = validationOptions.extnames;
- } else {
- validatedFile.allowedExtensions = await getEnabledExtensions();
- }
+ // if (validatedFile.allowedExtensions === undefined && validationOptions.extnames) {
+ // validatedFile.allowedExtensions = validationOptions.extnames;
+ // }
+ if (validatedFile.allowedExtensions === undefined && validationOptions.extnames !== undefined) {
+ validatedFile.allowedExtensions = validationOptions.extnames; // await getEnabledExtensions();
+ } else if (validatedFile.allowedExtensions === undefined && validationOptions.extnames === undefined) {
+ validatedFile.allowedExtensions = await getEnabledExtensions();
}
-
+ /**
+ * wieder lรถschen
+ * Set extensions when it's defined in the options and missing
+ * on the file instance
+ */
+ // if (file.clientNameSizeLimit === undefined && validationOptions.clientNameSizeLimit) {
+ // file.clientNameSizeLimit = validationOptions.clientNameSizeLimit;
+ // }
/**
* Validate file
*/
- try {
- validatedFile.validate();
- } catch (error) {
- field.report(`File validation failed: ${error.message}`, 'file.validation_error', field, validationOptions);
- return;
- }
-
+ validatedFile.validate();
/**
* Report errors
*/
@@ -142,37 +107,36 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op
const MULTIPART_FILE: typeof symbols.SUBTYPE = symbols.SUBTYPE;
export class VineMultipartFile extends BaseLiteralType {
+
[MULTIPART_FILE]: string;
- public validationOptions?: FileRuleValidationOptions;
+ // constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions) {
+ // super(options, [isMultipartFile(validationOptions || {})]);
+ // this.validationOptions = validationOptions;
+ // this.#private = true;
+ // }
+
+ // clone(): this {
+ // return new VineMultipartFile(this.validationOptions, this.cloneOptions()) as this;
+ // }
+ // #private;
+ // constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation[]);
+ // clone(): this;
+
+ public validationOptions;
// extnames: (18) ['gpkg', 'htm', 'html', 'csv', 'txt', 'asc', 'c', 'cc', 'h', 'srt', 'tiff', 'pdf', 'png', 'zip', 'jpg', 'jpeg', 'jpe', 'xlsx']
// size: '512mb'
+ // public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation[]) {
public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions) {
+ // super(options, validations);
super(options, [isMultipartFile(validationOptions || {})]);
this.validationOptions = validationOptions;
}
public clone(): any {
+ // return new VineMultipartFile(this.validationOptions, this.cloneOptions(), this.cloneValidations());
return new VineMultipartFile(this.validationOptions, this.cloneOptions());
}
-
- /**
- * Set maximum file size
- */
- public maxSize(size: string | number): this {
- const newOptions = { ...this.validationOptions, size };
- return new VineMultipartFile(newOptions, this.cloneOptions()) as this;
- }
-
- /**
- * Set allowed extensions
- */
- public extensions(extnames: string[]): this {
- const newOptions = { ...this.validationOptions, extnames };
- return new VineMultipartFile(newOptions, this.cloneOptions()) as this;
- }
-
-
}
export default class VinejsProvider {
@@ -191,8 +155,13 @@ export default class VinejsProvider {
/**
* The container bindings have booted
*/
+
boot(): void {
- Vine.macro('myfile', function (this: Vine, options?: FileRuleValidationOptions) {
+ // VineString.macro('translatedLanguage', function (this: VineString, options: Options) {
+ // return this.use(translatedLanguageRule(options));
+ // });
+
+ Vine.macro('myfile', function (this: Vine, options) {
return new VineMultipartFile(options);
});
@@ -206,41 +175,6 @@ export default class VinejsProvider {
}
return new RequestValidator(this.ctx).validateUsing(...args);
});
-
- // Ensure MIME validation macros are loaded
- this.loadMimeValidationMacros();
- this.loadFileScanMacros();
- this.loadFileLengthMacros();
- }
-
- /**
- * Load MIME validation macros - called during boot to ensure they're available
- */
- private async loadMimeValidationMacros(): Promise {
- try {
- // Dynamically import the MIME validation rule to ensure macros are registered
- await import('#start/rules/allowed_extensions_mimetypes');
- } catch (error) {
- console.warn('Could not load MIME validation macros:', error);
- }
- }
-
- private async loadFileScanMacros(): Promise {
- try {
- // Dynamically import the MIME validation rule to ensure macros are registered
- await import('#start/rules/file_scan');
- } catch (error) {
- console.warn('Could not load MIME validation macros:', error);
- }
- }
-
- private async loadFileLengthMacros(): Promise {
- try {
- // Dynamically import the MIME validation rule to ensure macros are registered
- await import('#start/rules/file_length');
- } catch (error) {
- console.warn('Could not load MIME validation macros:', error);
- }
}
/**
@@ -256,7 +190,5 @@ export default class VinejsProvider {
/**
* Preparing to shutdown the app
*/
- async shutdown() {
- clearExtensionsCache();
- }
+ async shutdown() {}
}
diff --git a/public/assets2/solr.sef.json b/public/assets2/solr.sef.json
index 096d58e..690f934 100644
--- a/public/assets2/solr.sef.json
+++ b/public/assets2/solr.sef.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/public/assets2/solr.xslt b/public/assets2/solr.xslt
index 4b3dc22..d4cac24 100644
--- a/public/assets2/solr.xslt
+++ b/public/assets2/solr.xslt
@@ -111,14 +111,7 @@
"server_date_modified": "
-
- ",
-
-
-
-
- "embargo_date": "
-
+
",
@@ -207,8 +200,7 @@
-
-
+
"
"
diff --git a/readme.md b/readme.md
index 7d032ce..0fd7e64 100644
--- a/readme.md
+++ b/readme.md
@@ -11,8 +11,6 @@ Welcome to the Tethys Research Repository Backend System! This is the backend co
- [Configuration](#configuration)
- [Database](#database)
- [API Documentation](#api-documentation)
-- [Commands](#commands)
-- [Documentation](#documentation)
- [Contributing](#contributing)
- [License](#license)
@@ -31,175 +29,5 @@ Before you begin, ensure you have met the following requirements:
1. Clone this repository:
```bash
- git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git
- cd tethys-backend
+ git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git
```
-
-2. Install dependencies:
-
- ```bash
- npm install
- ```
-
-3. Configure environment variables (see [Configuration](#configuration))
-
-4. Run database migrations:
-
- ```bash
- node ace migration:run
- ```
-
-5. Start the development server:
-
- ```bash
- npm run dev
- ```
-
-## Usage
-
-The Tethys Backend provides RESTful APIs for managing research datasets, user authentication, DOI registration, and search functionality.
-
-## Configuration
-
-Copy the `.env.example` file to `.env` and configure the following variables:
-
-### Database Configuration
-```bash
-DB_CONNECTION=pg
-DB_HOST=localhost
-DB_PORT=5432
-DB_USER=your_username
-DB_PASSWORD=your_password
-DB_DATABASE=tethys_db
-```
-
-### DataCite Configuration
-```bash
-# DataCite Credentials
-DATACITE_USERNAME=your_datacite_username
-DATACITE_PASSWORD=your_datacite_password
-DATACITE_PREFIX=10.21388
-
-# Environment-specific API endpoints
-DATACITE_API_URL=https://api.test.datacite.org # Test environment
-DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS
-
-# For production:
-# DATACITE_API_URL=https://api.datacite.org
-# DATACITE_SERVICE_URL=https://mds.datacite.org
-```
-
-### OpenSearch Configuration
-```bash
-OPENSEARCH_HOST=localhost:9200
-```
-
-### Application Configuration
-```bash
-BASE_DOMAIN=tethys.at
-APP_KEY=your_app_key
-```
-
-## Database
-
-The system uses PostgreSQL with Lucid ORM. Key models include:
-
-- **Dataset**: Research dataset metadata
-- **DatasetIdentifier**: DOI and other identifiers for datasets
-- **User**: User management and authentication
-- **XmlCache**: Cached XML metadata
-
-Run migrations and seeders:
-
-```bash
-# Run migrations
-node ace migration:run
-
-# Run seeders (if available)
-node ace db:seed
-```
-
-## API Documentation
-
-API endpoints are available for:
-
-- Dataset management (`/api/datasets`)
-- User authentication (`/api/auth`)
-- DOI registration (`/api/doi`)
-- Search functionality (`/api/search`)
-
-*Detailed API documentation can be found in the `/docs/api` directory.*
-
-## Commands
-
-The system includes several Ace commands for maintenance and data management:
-
-### Dataset Indexing
-```bash
-# Index all published datasets to OpenSearch
-node ace index:datasets
-
-# Index a specific dataset
-node ace index:datasets --publish_id 123
-```
-
-### DataCite DOI Management
-```bash
-# Update DataCite records for modified datasets
-node ace update:datacite
-
-# Show detailed statistics for datasets needing updates
-node ace update:datacite --stats
-
-# Preview what would be updated (dry run)
-node ace update:datacite --dry-run
-
-# Force update all DOI records
-node ace update:datacite --force
-
-# Update a specific dataset
-node ace update:datacite --publish_id 123
-```
-
-*For detailed command documentation, see the [Commands Documentation](docs/commands/)*
-
-## Documentation
-
-Comprehensive documentation is available in the `/docs` directory:
-
-- **[Commands Documentation](docs/commands/)** - Detailed guides for Ace commands
- - [DataCite Update Command](docs/commands/update-datacite.md) - DOI synchronization and management
- - [Dataset Indexing Command](docs/commands/index-datasets.md) - Search index management
-- **[API Documentation](docs/api/)** - REST API endpoints and usage
-- **[Deployment Guide](docs/deployment/)** - Production deployment instructions
-- **[Configuration Guide](docs/configuration/)** - Environment setup and configuration options
-
-## Contributing
-
-1. Fork the repository
-2. Create a feature branch (`git checkout -b feature/amazing-feature`)
-3. Commit your changes (`git commit -m 'Add some amazing feature'`)
-4. Push to the branch (`git push origin feature/amazing-feature`)
-5. Open a Pull Request
-
-### Development Guidelines
-
-- Follow the existing code style and conventions
-- Write tests for new features
-- Update documentation for any API changes
-- Ensure all commands and migrations work properly
-
-### Testing Commands
-
-```bash
-# Run tests
-npm test
-
-# Test specific commands
-node ace update:datacite --dry-run --publish_id 123
-node ace index:datasets --publish_id 123
-```
-
-## License
-
-This project is licensed under the [MIT License](LICENSE).
\ No newline at end of file
diff --git a/resources/js/Components/BaseButton.vue b/resources/js/Components/BaseButton.vue
index 1462566..74c0b5d 100644
--- a/resources/js/Components/BaseButton.vue
+++ b/resources/js/Components/BaseButton.vue
@@ -1,5 +1,5 @@
-
{{ label }}
diff --git a/resources/js/Components/CardBox.vue b/resources/js/Components/CardBox.vue
index dbdee01..c2d200e 100644
--- a/resources/js/Components/CardBox.vue
+++ b/resources/js/Components/CardBox.vue
@@ -67,7 +67,7 @@ const submit = (e) => {
{{ title }}
-